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• Conference paper
  Walker M, Hall A, Anderson RM, Basanez M-Get al., 2008,

  FACTORS AFFECTING THE FECUNDITY OF <i>ASCARIS LUMBRICOIDES</i> AND THEIR IMPACT ON PATTERNS OF DENSITY DEPENDENCE

  , 57th Annual Meeting of the American-Society-of-Tropical-Medicine-and-Hygiene, Publisher: AMER SOC TROP MED & HYGIENE, Pages: 337-337, ISSN: 0002-9637
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• Conference paper
  Schnall-Levin M, Chindelevitch L, Berger B, 2008,

  Inverting the viterbi algorithm: An abstract framework for structure design

  , Pages: 904-911

  Probabilistic grammatical formalisms such as hidden Markov models (HMMs) and stochastic context-free grammars (SCFGs) have been extensively studied and widely applied in a number of fields. Here, we introduce a new algorithmic problem on HMMs and SCFGs that arises naturally from protein and RNA design, and which has not been previously studied. The problem can be viewed as an inverse to the one solved by the Viterbi algorithm on HMMs or by the CKY algorithm on SCFGs. We study this problem theoretically and obtain the first algorithmic results. We prove that the problem is NP-complete, even for a 3-letter emission alphabet, via a reduction from 3-SAT, a result that has implications for the hardness of RNA secondary structure design. We then develop a number of approaches for making the problem tractable. In particular, for HMMs we develop a branch-and-bound algorithm, which can be shown to have fixed-parameter tractable worst-case running time, exponential in the number of states of the HMM but linear in the length of the structure. We also show how to cast the problem as a Mixed Integer Linear Program. Copyright 2008 by the author(s)/owner(s).

  • Abstract
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  • Citations: 26
• Journal article
  Sabatelli L, Ghani AC, Rodrigues LC, Hotez PJ, Brooker Set al., 2008,

  Modelling heterogeneity and the impact of chemotherapy and vaccination against human hookworm

  , JOURNAL OF THE ROYAL SOCIETY INTERFACE, Vol: 5, Pages: 1329-1341, ISSN: 1742-5689
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  • Citations: 15
• Journal article
  Ball FG, Knock ES, O'Neill PD, 2008,

  Control of emerging infectious diseases using responsive imperfect vaccination and isolation

  , MATHEMATICAL BIOSCIENCES, Vol: 216, Pages: 100-113, ISSN: 0025-5564
  • Author Web Link
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  • Citations: 21
• Journal article
  Trotter C, Scott P, Huss A, Egger Met al., 2008,

  Pneumococcal polysaccharide vaccine effectiveness: study quality must not be ignored

  , LANCET INFECTIOUS DISEASES, Vol: 8, Pages: 664-664, ISSN: 1473-3099
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  • Citations: 4
• Journal article
  Rhodes CJ, Anderson RM, 2008,

  Contact rate calculation for a basic epidemic model

  , MATHEMATICAL BIOSCIENCES, Vol: 216, Pages: 56-62, ISSN: 0025-5564
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  • Citations: 27
• Journal article
  Basanez M-G, 2008,

  Mathematical modelling of parasitic infections: from data and parameter estimation to evolutionary implications

  , PARASITOLOGY, Vol: 135, Pages: 1487-1488, ISSN: 0031-1820
  • Author Web Link
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  • Citations: 1
• Journal article
  Rudge JW, Carabin H, Balolong E, Tallo V, Shrivastava J, Lu D-B, Basanez M-G, Olveda R, McGarvey ST, Webster JPet al., 2008,

  Population Genetics of <i>Schistosoma japonicum</i> within the Philippines Suggest High Levels of Transmission between Humans and Dogs

  , PLOS NEGLECTED TROPICAL DISEASES, Vol: 2, ISSN: 1935-2735
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  • Citations: 61
• Journal article
  Bottomley C, Isham V, Collins RC, Basanez M-Get al., 2008,

  Rates of microfilarial production by <i>Onchocerca volvulus</i> are not cumulatively reduced by multiple ivermectin treatments

  , PARASITOLOGY, Vol: 135, Pages: 1571-1581, ISSN: 0031-1820
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  • Citations: 25
• Journal article
  Pellis L, Ferguson NM, Fraser C, 2008,

  The relationship between real-time and discrete-generation models of epidemic spread

  , Mathematical Biosciences, Vol: 216, Pages: 63-70, ISSN: 0025-5564
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