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Comment
. 2008 Jan;4(1):e25.
doi: 10.1371/journal.pcbi.0040025.

Comparison of immunogen designs that optimize peptide coverage: reply to Fischer et al

David C Nickle, Nebojsa Jojic, David Heckerman, Vladimir Jojic, Darko Kirovski, Morgane Rolland, Sergei Kosakovsky Pond, James I Mullins
Comment

Comparison of immunogen designs that optimize peptide coverage: reply to Fischer et al

David C Nickle et al. PLoS Comput Biol. 2008 Jan.

Erratum in

No abstract available

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Comparison of Peptide Coverage Scores Achievable with Different Immunogen Formats and Algorithms
In (A) and (B), we show the coverage for Gag and Nef, respectively, as a function of immunogen gene length for different immunogen formats. Natural strains: a cocktail of natural HIV sequences optimized for breadth of diversity by Gibbs sampling. Mosaics: a cocktail of constructs collinear with natural strains optimized by the code developed by Fischer et al. [3]. Greedy COT+: COT+ sequences were optimized by a simple greedy algorithm described by Jojic et al. [2,13] and Nickle et al. [1]. Optimized COT+: a stochastic combinatorial optimization of COT+ using the algorithm of Kirovski et al. [5], run on a 300 node Windows HPC cluster for one day. Unconstrained: a sequence optimized for coverage with the Kirovski algorithm without regard to gene collinearity. To emphasize that some of the constructs can be optimized at fractional lengths, those results are shown by lines (since points on the line are achievable), while the constructs consisting of an integer number of strains are shown as dots only.
See this image and copyright information in PMC

Comment on

  • Coping with viral diversity in HIV vaccine design.
    Nickle DC, Rolland M, Jensen MA, Pond SL, Deng W, Seligman M, Heckerman D, Mullins JI, Jojic N. Nickle DC, et al. PLoS Comput Biol. 2007 Apr 27;3(4):e75. doi: 10.1371/journal.pcbi.0030075. PLoS Comput Biol. 2007. PMID: 17465674 Free PMC article.

References

    1. Nickle DC, Rolland M, Jensen MA, Pond SL, Deng W, et al. Coping with viral diversity in HIV vaccine design. PLoS Comput Biol. 2007;3:e75. doi: . - DOI - PMC - PubMed
    1. Jojic N, Jojic V, Frey B, Meek C, Heckerman D. Using epitomes to model genetic diversity: Rational design of HIV vaccine cocktails; Proceedings of the 19th Annual Conference on Neural Information Processing Systems; 5–10 December 2005;; Whistler, British Columbia, Canada: 2005.
    1. Fischer W, Perkins S, Theiler J, Bhattacharya T, Yusim K, et al. Polyvalent vaccines for optimal coverage of potential T-cell epitopes in global HIV-1 variants. Nat Med. 2007;13:100–106. - PubMed
    1. Fischer W, Liao HX, Haynes BF, Letvin NL, Korber B. Coping with viral diversity in HIV vaccine design: A response to Nickle et al. PLoS Comput Biol. 2007;4:e15. doi: . - DOI - PMC - PubMed
    1. Kirovski D, Heckerman D, Jojic N. Combinatorics of the vaccine design problem: Definition and an algorithm. Microsoft Research Technical Report MSR-TR-2007–2148. 2007.