@article{4228,
  abstract     = {Suppressive drug interactions, in which one antibiotic can actually help bacterial cells to grow faster in the presence of another, occur between protein and DNA synthesis inhibitors. Here, we show that this suppression results from nonoptimal regulation of ribosomal genes in the presence of DNA stress. Using GFP-tagged transcription reporters in Escherichia coli, we find that ribosomal genes are not directly regulated by DNA stress, leading to an imbalance between cellular DNA and protein content. To test whether ribosomal gene expression under DNA stress is nonoptimal for growth rate, we sequentially deleted up to six of the seven ribosomal RNA operons. These synthetic manipulations of ribosomal gene expression correct the protein-DNA imbalance, lead to improved survival and growth, and completely remove the suppressive drug interaction. A simple mathematical model explains the nonoptimal regulation in different nutrient environments. These results reveal the genetic mechanism underlying an important class of suppressive drug interactions.},
  author       = {Bollenbach, Tobias and Quan, Selwyn and Remy Chait and Kishony, Roy},
  journal      = {Cell},
  number       = {4},
  pages        = {707 -- 718},
  publisher    = {Cell Press},
  title        = {{Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions}},
  doi          = {10.1016/j.cell.2009.10.025},
  volume       = {139},
  year         = {2009},
}

@article{4231,
  abstract     = {The evolution of quantitative characters depends on the frequencies of the alleles involved, yet these frequencies cannot usually be measured. Previous groups have proposed an approximation to the dynamics of quantitative traits, based on an analogy with statistical mechanics. We present a modified version of that approach, which makes the analogy more precise and applies quite generally to describe the evolution of allele frequencies. We calculate explicitly how the macroscopic quantities (i.e., quantities that depend on the quantitative trait) depend on evolutionary forces, in a way that is independent of the microscopic details. We first show that the stationary distribution of allele frequencies under drift, selection, and mutation maximizes a certain measure of entropy, subject to constraints on the expectation of observable quantities. We then approximate the dynamical changes in these expectations, assuming that the distribution of allele frequencies always maximizes entropy, conditional on the expected values. When applied to directional selection on an additive trait, this gives a very good approximation to the evolution of the trait mean and the genetic variance, when the number of mutations per generation is sufficiently high (4Nμ > 1). We show how the method can be modified for small mutation rates (4Nμ → 0). We outline how this method describes epistatic interactions as, for example, with stabilizing selection.},
  author       = {Barton, Nicholas H and De Vladar, Harold},
  journal      = {Genetics},
  number       = {3},
  pages        = {997 -- 1011},
  publisher    = {Genetics Society of America},
  title        = {{Statistical mechanics and the evolution of polygenic quantitative traits}},
  doi          = {10.1534/genetics.108.099309},
  volume       = {181},
  year         = {2009},
}

@phdthesis{4232,
  author       = {Harold Vladar},
  publisher    = {Faculty of mathematical and natural sciences, University of Groningen},
  title        = {{Stochasticity and Variability in the dynamics and genetics of populations}},
  doi          = {3811},
  year         = {2009},
}

@article{4242,
  abstract     = {Felsenstein distinguished two ways by which selection can directly strengthen isolation. First, a modifier that strengthens prezygotic isolation can be favored everywhere. This fits with the traditional view of reinforcement as an adaptation to reduce deleterious hybridization by strengthening assortative mating. Second, selection can favor association between different incompatibilities, despite recombination. We generalize this “two allele” model to follow associations among any number of incompatibilities, which may include both assortment and hybrid inviability. Our key argument is that this process, of coupling between incompatibilities, may be quite different from the usual view of reinforcement: strong isolation can evolve through the coupling of any kind of incompatibility, whether prezygotic or postzygotic. Single locus incompatibilities become coupled because associations between them increase the variance in compatibility, which in turn increases mean fitness if there is positive epistasis. Multiple incompatibilities, each maintained by epistasis, can become coupled in the same way. In contrast, a single-locus incompatibility can become coupled with loci that reduce the viability of haploid hybrids because this reduces harmful recombination. We obtain simple approximations for the limits of tight linkage, and strong assortment, and show how assortment alleles can invade through associations with other components of reproductive isolation.},
  author       = {Barton, Nicholas H and De Cara, Maria},
  journal      = {Evolution; International Journal of Organic Evolution},
  number       = {5},
  pages        = {1171 -- 1190},
  publisher    = {Wiley},
  title        = {{The evolution of strong reproductive isolation}},
  doi          = {10.1111/j.1558-5646.2009.00622.x},
  volume       = {63},
  year         = {2009},
}

@article{4357,
  abstract     = {Parallel evolution is the acquisition of identical adaptive traits in independently evolving populations. Understanding whether the genetic changes underlying adaptation to a common selective environment are parallel within and between species is interesting because it sheds light on the degree of evolutionary constraints. If parallel evolution is perfect, then the implication is that forces such as functional constraints, epistasis, and pleiotropy play an important role in shaping the outcomes of adaptive evolution. In addition, population genetic theory predicts that the probability of parallel evolution will decline with an increase in the number of adaptive solutions-if a single adaptive solution exists, then parallel evolution will be observed among highly divergent species. For this reason, it is predicted that close relatives-which likely overlap more in the details of their adaptive solutions-will show more parallel evolution. By adapting three related bacteriophage species to a novel environment we find (1) a high rate of parallel genetic evolution at orthologous nucleotide and amino acid residues within species, (2) parallel beneficial mutations do not occur in a common order in which they fix or appear in an evolving population, (3) low rates of parallel evolution and convergent evolution between species, and (4) the probability of parallel and convergent evolution between species is strongly effected by divergence.},
  author       = {Jonathan Bollback and Huelsenbeck, John P},
  journal      = {Genetics},
  number       = {1},
  pages        = {225 -- 234},
  publisher    = {Genetics Society of America},
  title        = {{Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence}},
  doi          = {10.1534/genetics.107.085225},
  volume       = {181},
  year         = {2009},
}

@inproceedings{4360,
  author       = {Thomas Wies and Piskac, Ruzica and Kuncak, Viktor},
  pages        = {366 -- 382},
  publisher    = {Springer},
  title        = {{Combining Theories with Shared Set Operations}},
  doi          = {1558},
  year         = {2009},
}

@phdthesis{4363,
  author       = {Vasu Singh},
  booktitle    = {Formalizing and Verifying Transactional Memories},
  publisher    = {EPFL Lausanne},
  title        = {{Formalizing and Verifying Transactional Memories}},
  year         = {2009},
}

@inproceedings{4365,
  author       = {Seghir,Mohamed Nassim and Podelski,Andreas and Thomas Wies},
  pages        = {3 -- 18},
  publisher    = {Springer},
  title        = {{Abstraction Refinement for Quantified Array Assertions}},
  doi          = {1556},
  year         = {2009},
}

@inproceedings{4375,
  author       = {Lahiri,Shuvendu K. and Qadeer,Shaz and Galeotti,Juan P. and Voung,Jan W. and Thomas Wies},
  pages        = {493 -- 508},
  publisher    = {Springer},
  title        = {{Intra-module Inference}},
  doi          = {1555},
  year         = {2009},
}

@inproceedings{4376,
  author       = {Lublinerman,Roberto and Chaudhuri,Swarat and Pavol Cerny},
  pages        = {61 -- 80},
  publisher    = {ACM},
  title        = {{Parallel programming with object assemblies}},
  doi          = {1546},
  year         = {2009},
}

@inproceedings{4377,
  author       = {Hoenicke,Jochen and Leino, K Rustan and Podelski,Andreas and Schäf,Martin and Thomas Wies},
  pages        = {338 -- 353},
  publisher    = {Springer},
  title        = {{It's Doomed; We Can Prove It}},
  doi          = {1557},
  year         = {2009},
}

@inproceedings{4383,
  abstract     = {Pseudo-code descriptions of STMs assume sequentially consistent program execution and atomicity of high-level STM operations like read, write, and commit. These assumptions are often violated in realistic settings, as STM implementations run on relaxed memory models, with the atomicity of operations as provided by the hardware. This paper presents the first approach to verify STMs under relaxed memory models with atomicity of 32 bit loads and stores, and read-modify-write operations. We present RML, a new high-level language for expressing concurrent algorithms with a hardware-level atomicity of instructions, and whose semantics is parametrized by various relaxed memory models. We then present our tool, FOIL, which takes as input the RML description of an STM algorithm and the description of a memory model, and automatically determines the locations of fences, which if inserted, ensure the correctness of the STM algorithm under the given memory model. We use FOIL to verify DSTM, TL2, and McRT STM under the memory models of sequential consistency, total store order, partial store order, and relaxed memory order.},
  author       = {Guerraoui, Rachid and Thomas Henzinger and Vasu Singh},
  pages        = {321 -- 336},
  publisher    = {Springer},
  title        = {{Software transactional memory on relaxed memory models}},
  doi          = {10.1007/978-3-642-02658-4_26},
  volume       = {5643},
  year         = {2009},
}

@inproceedings{4385,
  author       = {Dragojevic,Aleksandar and Guerraoui, Rachid and Singh, Anmol V and Vasu Singh},
  pages        = {7 -- 16},
  publisher    = {ACM},
  title        = {{Preventing versus curing: avoiding conflicts in transactional memories}},
  doi          = {1533},
  year         = {2009},
}

@inproceedings{4391,
  author       = {Pavol Cerny and Alur, Rajeev},
  pages        = {173 -- 187},
  publisher    = {Springer},
  title        = {{Automated Analysis of Java Methods for Confidentiality}},
  doi          = {1548},
  year         = {2009},
}

@inproceedings{4403,
  abstract     = {For programs whose data variables range over boolean or finite domains, program verification is decidable, and this forms the basis of recent tools for software model checking. In this paper, we consider algorithmic verification of programs that use boolean variables, and in addition, access a single read-only array whose length is potentially unbounded, and whose elements range over a potentially unbounded data domain. We show that the reachability problem, while undecidable in general, is (1) Pspace-complete for programs in which the array-accessing for-loops are not nested, (2) decidable for a restricted class of programs with doubly-nested loops. The second result establishes connections to automata and logics defining languages over data words.},
  author       = {Alur, Rajeev and Cerny, Pavol and Weinstein, Scott},
  location     = {Coimbra, Portugal},
  pages        = {86 -- 101},
  publisher    = {Springer},
  title        = {{Algorithmic analysis of array-accessing programs}},
  doi          = {10.1007/978-3-642-04027-6_9},
  volume       = {5771},
  year         = {2009},
}

@inproceedings{4453,
  abstract     = {We present an on-the-fly abstraction technique for infinite-state continuous -time Markov chains. We consider Markov chains that are specified by a finite set of transition classes. Such models naturally represent biochemical reactions and therefore play an important role in the stochastic modeling of biological systems. We approximate the transient probability distributions at various time instances by solving a sequence of dynamically constructed abstract models, each depending on the previous one. Each abstract model is a finite Markov chain that represents the behavior of the original, infinite chain during a specific time interval. Our approach provides complete information about probability distributions, not just about individual parameters like the mean. The error of each abstraction can be computed, and the precision of the abstraction refined when desired. We implemented the algorithm and demonstrate its usefulness and efficiency on several case studies from systems biology.},
  author       = {Thomas Henzinger and Maria Mateescu and Wolf, Verena},
  pages        = {337 -- 352},
  publisher    = {Springer},
  title        = {{Sliding-window abstraction for infinite Markov chains}},
  doi          = {10.1007/978-3-642-02658-4_27},
  volume       = {5643},
  year         = {2009},
}

@inproceedings{4535,
  abstract     = {Molecular noise, which arises from the randomness of the discrete events in the cell, significantly influences fundamental biological processes. Discrete -state continuous-time stochastic models (CTMC) can be used to describe such effects, but the calculation of the probabilities of certain events is computationally expensive.
We present a comparison of two analysis approaches for CTMC. On one hand, we estimate the probabilities of interest using repeated Gillespie simulation and determine the statistical accuracy that we obtain. On the other hand, we apply a numerical reachability analysis that approximates the probability distributions of the system at several time instances. We use examples of cellular processes to demonstrate the superiority of the reachability analysis if accurate results are required.},
  author       = {Didier, Frédéric and Thomas Henzinger and Maria Mateescu and Wolf, Verena},
  pages        = {173 -- 188},
  publisher    = {Springer},
  title        = {{Approximation of event probabilities in noisy cellular processes}},
  doi          = {10.1007/978-3-642-03845-7_12},
  volume       = {5688},
  year         = {2009},
}

@inproceedings{4540,
  abstract     = {Weighted automata are nondeterministic automata with numerical weights on transitions. They can define quantitative languages L that assign to each word w a real number L(w). In the case of infinite words, the value of a run is naturally computed as the maximum, limsup, liminf, limit average, or discounted sum of the transition weights. We study expressiveness and closure questions about these quantitative languages. We first show that the set of words with value greater than a threshold can be non-w-regular for deterministic limit-average and discounted-sum automata, while this set is always w-regular when the threshold is isolated (i.e., some neighborhood around the threshold contains no word). In the latter case, we prove that the w-regular language is robust against small perturbations of the transition weights. We next consider automata with transition weights 0 or 1 and show that they are as expressive as general weighted automata in the limit-average case, but not in the discounted-sum case. Third, for quantitative languages L-1 and L-2, we consider the operations max(L-1, L-2), min(L-1, L-2), and 1-L-1, which generalize the boolean operations on languages, as well as the sum L-1 + L-2. We establish the closure properties of all classes of quantitative languages with respect to these four operations.},
  author       = {Chatterjee, Krishnendu and Doyen, Laurent and Henzinger, Thomas A},
  pages        = {199 -- 208},
  publisher    = {IEEE},
  title        = {{Expressiveness and closure properties for quantitative languages}},
  doi          = {10.1109/LICS.2009.16},
  year         = {2009},
}

@inproceedings{4542,
  abstract     = {Weighted automata are finite automata with numerical weights on transitions. Nondeterministic weighted automata define quantitative languages L that assign to each word w a real number L(w) computed as the maximal value of all runs over w, and the value of a run r is a function of the sequence of weights that appear along r. There are several natural functions to consider such as Sup, LimSup, LimInf, limit average, and discounted sum of transition weights.
We introduce alternating weighted automata in which the transitions of the runs are chosen by two players in a turn-based fashion. Each word is assigned the maximal value of a run that the first player can enforce regardless of the choices made by the second player. We survey the results about closure properties, expressiveness, and decision problems for nondeterministic weighted automata, and we extend these results to alternating weighted automata.
For quantitative languages L 1 and L 2, we consider the pointwise operations max(L 1,L 2), min(L 1,L 2), 1 − L 1, and the sum L 1 + L 2. We establish the closure properties of all classes of alternating weighted automata with respect to these four operations.
We next compare the expressive power of the various classes of alternating and nondeterministic weighted automata over infinite words. In particular, for limit average and discounted sum, we show that alternation brings more expressive power than nondeterminism.
Finally, we present decidability results and open questions for the quantitative extension of the classical decision problems in automata theory: emptiness, universality, language inclusion, and language equivalence.},
  author       = {Chatterjee, Krishnendu and Doyen, Laurent and Henzinger, Thomas A},
  location     = {Wroclaw, Poland},
  pages        = {3 -- 13},
  publisher    = {Springer},
  title        = {{Alternating weighted automata}},
  doi          = {10.1007/978-3-642-03409-1_2},
  volume       = {5699},
  year         = {2009},
}

@inproceedings{4543,
  abstract     = {The synthesis of a reactive system with respect to all omega-regular specification requires the solution of a graph game. Such games have been extended in two natural ways. First, a game graph can be equipped with probabilistic choices between alternative transitions, thus allowing the, modeling of uncertain behaviour. These are called stochastic games. Second, a liveness specification can he strengthened to require satisfaction within all unknown but bounded amount of time. These are called finitary objectives. We study. for the first time, the, combination of Stochastic games and finitary objectives. We characterize the requirements on optimal strategies and provide algorithms for Computing the maximal achievable probability of winning stochastic games with finitary parity or Street, objectives. Most notably the set of state's from which a player can win with probability . for a finitary parity objective can he computed in polynomial time even though no polynomial-time algorithm is known in the nonfinitary case.},
  author       = {Chatterjee, Krishnendu and Henzinger, Thomas A and Horn, Florian},
  location     = {High Tatras, Slovakia},
  pages        = {34 -- 54},
  publisher    = {Springer},
  title        = {{Stochastic games with finitary objectives}},
  doi          = {10.1007/978-3-642-03816-7_4},
  volume       = {5734},
  year         = {2009},
}