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- Statistical alignment based on fragment insertion and deletion models (2002)
- Motivation: The topic of this paper is the estimation of alignments and mutation rates based on stochastic sequence-evolution models that allow insertions and deletions of subsequences ("fragments") and not just single bases. The model we propose is a variant of a model introduced by Thorne, Kishino, and Felsenstein (1992). The computational tractability of the model depends on certain restrictions in the insertion/deletion process; possible effects we discuss. Results: The process of fragment insertion and deletion in the sequence-evolution model induces a hidden Markov structure at the level of alignments and thus makes possible efficient statistical alignment algorithms. As an example we apply a sampling procedure to assess the variability in alignment and mutation parameter estimates for HVR1 sequences of human and orangutan, improving results of previous work. Simulation studies give evidence that estimation methods based on the proposed model also give satisfactory results when applied to data for which the restrictions in the insertion/deletion process do not hold. Availability: The source code of the software for sampling alignments and mutation rates for a pair of DNA sequences according to the fragment insertion and deletion model is freely available from www.math.uni-frankfurt.de/~stoch/software/mcmcsalut under the terms of the GNU public license (GPL, 2000).

- The representation problem based on factoring (2002)
- We review the representation problem based on factoring and show that this problem gives rise to alternative solutions to a lot of cryptographic protocols in the literature. And, while the solutions so far usually either rely on the RSA problem or the intractability of factoring integers of a special form (e.g., Blum integers), the solutions here work with the most general factoring assumption. Protocols we discuss include identification schemes secure against parallel attacks, secure signatures, blind signatures and (non-malleable) commitments.

- On the impossibility of constructing non-interactive statistically-secret protocols from any trapdoor one-way function (2002)
- We show that non-interactive statistically-secret bit commitment cannot be constructed from arbitrary black-box one-to-one trapdoor functions and thus from general public-key cryptosystems. Reducing the problems of non-interactive crypto-computing, rerandomizable encryption, and non-interactive statistically-sender-private oblivious transfer and low-communication private information retrieval to such commitment schemes, it follows that these primitives are neither constructible from one-to-one trapdoor functions and public-key encryption in general. Furthermore, our separation sheds some light on statistical zeroknowledge proofs. There is an oracle relative to which one-to-one trapdoor functions and one-way permutations exist, while the class of promise problems with statistical zero-knowledge proofs collapses in P. This indicates that nontrivial problems with statistical zero-knowledge proofs require more than (trapdoor) one-wayness.