School of Mathematics and Statistics - Research Publications
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ItemBioconductor: open software development for computational biology and bioinformatics(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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ItemA 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(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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ItemNo Preview AvailableAsymmetrically gauged WZNW models(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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ItemNo Preview AvailableAsymmetric cosets(SPRINGER, 2003-02)
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ItemA note on the equality of algebraic and geometric D-brane charges in WZW models(SPRINGER, 2004-05)
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ItemGametic phase estimation over large genomic regions using an adaptive window approach.(Springer Science and Business Media LLC, 2003-11)The authors present ELB, an easy to programme and computationally fast algorithm for inferring gametic phase in population samples of multilocus genotypes. Phase updates are made on the basis of a window of neighbouring loci, and the window size varies according to the local level of linkage disequilibrium. Thus, ELB is particularly well suited to problems involving many loci and/or relatively large genomic regions, including those with variable recombination rate. The authors have simulated population samples of single nucleotide polymorphism genotypes with varying levels of recombination and marker density, and find that ELB provides better local estimation of gametic phase than the PHASE or HTYPER programs, while its global accuracy is broadly similar. The relative improvement in local accuracy increases both with increasing recombination and with increasing marker density. Short tandem repeat (STR, or microsatellite) simulation studies demonstrate ELB's superiority over PHASE both globally and locally. Missing data are handled by ELB; simulations show that phase recovery is virtually unaffected by up to 2 per cent of missing data, but that phase estimation is noticeably impaired beyond this amount. The authors also applied ELB to datasets obtained from random pairings of 42 human X chromosomes typed at 97 diallelic markers in a 200 kb low-recombination region. Once again, they found ELB to have consistently better local accuracy than PHASE or HTYPER, while its global accuracy was close to the best.
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ItemThe Orevkov invariant of an affine plane curve(AMER MATHEMATICAL SOC, 2003)
We show that although the fundamental group of the complement of an algebraic affine plane curve is not easy to compute, it possesses a more accessible quotient, which we call the Orevkov invariant.
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ItemLocalising Dehn's lemma and the loop theorem in 3-manifolds(CAMBRIDGE UNIV PRESS, 2004-09)
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ItemHecke eigenvalues of Siegel modular forms (mod p) and of algebraic modular forms(ACADEMIC PRESS INC ELSEVIER SCIENCE, 2004-06)
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ItemCoxeter groups act on CAT(0) cube complexes(WALTER DE GRUYTER & CO, 2003)