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3853 Publications

2010 | Conference Paper | IST-REx-ID: 4362
V. Singh, “Runtime verification for software transactional memories,” presented at the RV: International Conference on Runtime Verification, St. Julians, Malta, 2010, vol. 6418, pp. 421–435.
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2010 | Conference Paper | IST-REx-ID: 4369 | OA
D. Nickovic and N. Piterman, “From MTL to deterministic timed automata,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Klosterneuburg, Austria, 2010, vol. 6246, pp. 152–167.
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2010 | Conference Paper | IST-REx-ID: 4378 | OA
V. Kuncak, R. Piskac, P. Suter, and T. Wies, “Building a calculus of data structures,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Madrid, Spain, 2010, vol. 5944, pp. 26–44.
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2010 | Conference Paper | IST-REx-ID: 4380 | OA
T. A. Henzinger, A. Tomar, V. Singh, T. Wies, and D. Zufferey, “A marketplace for cloud resources,” presented at the EMSOFT: Embedded Software , Arizona, USA, 2010, pp. 1–8.
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2010 | Conference Paper | IST-REx-ID: 4381 | OA
T. A. Henzinger, A. Tomar, V. Singh, T. Wies, and D. Zufferey, “FlexPRICE: Flexible provisioning of resources in a cloud environment,” presented at the CLOUD: Cloud Computing, Miami, USA, 2010, pp. 83–90.
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2010 | Conference Paper | IST-REx-ID: 4382 | OA
R. Guerraoui, T. A. Henzinger, M. Kapalka, and V. Singh, “Transactions in the jungle,” presented at the SPAA: ACM Symposium on Parallel Algorithms and Architectures, Santorini, Greece, 2010, pp. 263–272.
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2010 | Conference Paper | IST-REx-ID: 4388 | OA
K. Chatterjee, T. A. Henzinger, B. Jobstmann, and A. Radhakrishna, “GIST: A solver for probabilistic games,” presented at the CAV: Computer Aided Verification, Edinburgh, UK, 2010, vol. 6174, pp. 665–669.
View | Files available | DOI | arXiv
 
2010 | Conference Paper | IST-REx-ID: 4389 | OA
L. Doyen, T. A. Henzinger, A. Legay, and D. Nickovic, “Robustness of sequential circuits,” presented at the ACSD: Application of Concurrency to System Design, 2010, pp. 77–84.
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2010 | Conference Paper | IST-REx-ID: 4390 | OA
P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, and R. Alur, “Model checking of linearizability of concurrent list implementations,” presented at the CAV: Computer Aided Verification, Edinburgh, UK, 2010, vol. 6174, pp. 465–479.
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2010 | Book Chapter | IST-REx-ID: 4392
P. Cerny, T. A. Henzinger, and A. Radhakrishna, “Quantitative Simulation Games,” in Time For Verification: Essays in Memory of Amir Pnueli, vol. 6200, Z. Manna and D. Peled, Eds. Springer, 2010, pp. 42–60.
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2010 | Conference Paper | IST-REx-ID: 4393 | OA
P. Cerny, T. A. Henzinger, and A. Radhakrishna, “Simulation distances,” presented at the CONCUR: Concurrency Theory, Paris, France, 2010, vol. 6269, pp. 235–268.
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2010 | Conference Paper | IST-REx-ID: 4396 | OA
D. Beyer, T. A. Henzinger, G. Théoduloz, and D. Zufferey, “Shape refinement through explicit heap analysis,” presented at the FASE: Fundamental Approaches To Software Engineering, Paphos, Cyprus, 2010, vol. 6013, pp. 263–277.
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2010 | Conference Paper | IST-REx-ID: 10909
C. Chen and D. Freedman, “Hardness results for homology localization,” in Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms, Austin, TX, United States, 2010, pp. 1594–1604.
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2010 | Conference Paper | IST-REx-ID: 10908 | OA
R. Blanc, T. A. Henzinger, T. Hottelier, and L. Kovács, “ABC: Algebraic Bound Computation for loops,” in Logic for Programming, Artificial Intelligence, and Reasoning, Dakar, Senegal, 2010, vol. 6355, pp. 103–118.
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2009 | Conference Paper | IST-REx-ID: 4542 | OA
K. Chatterjee, L. Doyen, and T. A. Henzinger, “Alternating weighted automata,” presented at the FCT: Fundamentals of Computation Theory, Wroclaw, Poland, 2009, vol. 5699, pp. 3–13.
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2009 | Conference Paper | IST-REx-ID: 4543
K. Chatterjee, T. A. Henzinger, and F. Horn, “Stochastic games with finitary objectives,” presented at the MFCS: Mathematical Foundations of Computer Science, High Tatras, Slovakia, 2009, vol. 5734, pp. 34–54.
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2009 | Conference Paper | IST-REx-ID: 4545 | OA
K. Chatterjee, L. Doyen, and T. A. Henzinger, “A survey of stochastic games with limsup and liminf objectives,” presented at the ICALP: Automata, Languages and Programming, Rhodos, Greece, 2009, vol. 5556, pp. 1–15.
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2009 | Conference Paper | IST-REx-ID: 4569 | OA
R. Bloem, K. Chatterjee, T. A. Henzinger, and B. Jobstmann, “Better quality in synthesis through quantitative objectives,” presented at the CAV: Computer Aided Verification, Grenoble, France, 2009, vol. 5643, pp. 140–156.
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2009 | Technical Report | IST-REx-ID: 5392 | OA
K. Chatterjee, Probabilistic automata on infinite words: Decidability and undecidability results. IST Austria, 2009.
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2009 | Technical Report | IST-REx-ID: 5393 | OA
K. Chatterjee, T. A. Henzinger, B. Jobstmann, and A. Radhakrishna, Gist: A solver for probabilistic games. IST Austria, 2009.
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2009 | Technical Report | IST-REx-ID: 5394 | OA
K. Chatterjee, T. A. Henzinger, and F. Horn, Improved lower bounds for request-response and finitary Streett games. IST Austria, 2009.
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2009 | Technical Report | IST-REx-ID: 5395 | OA
K. Chatterjee, L. Doyen, and T. A. Henzinger, Qualitative analysis of partially-observable Markov decision processes. IST Austria, 2009.
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2009 | Journal Article | IST-REx-ID: 9453 | OA
T.-F. Hsieh et al., “Genome-wide demethylation of Arabidopsis endosperm,” Science, vol. 324, no. 5933. American Association for the Advancement of Science, pp. 1451–1454, 2009.
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2009 | Book Chapter | IST-REx-ID: 3675
N. H. Barton, “Why sex and recombination? ,” in Cold Spring Harbor Symposia on Quantitative Biology, vol. 74, Cold Spring Harbor Laboratory Press, 2009, pp. 187–195.
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2009 | Journal Article | IST-REx-ID: 3775 | OA
N. H. Barton and J. Coe, “On the application of statistical physics to evolutionary biology,” Journal of Theoretical Biology, vol. 259, no. 2. Elsevier, pp. 317–324, 2009.
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2009 | Journal Article | IST-REx-ID: 3780 | OA
A. Davison, N. H. Barton, and B. Clarke, “The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails,” Journal of Evolutionary Biology, vol. 22, no. 8. Wiley, pp. 1624–1635, 2009.
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2009 | Conference Paper | IST-REx-ID: 3837 | OA
S. Tripakis, B. Lickly, T. A. Henzinger, and E. Lee, “On relational interfaces,” in EMSOFT ’09 Proceedings of the seventh ACM international conference on Embedded software, Grenoble, France, 2009, pp. 67–76.
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2009 | Conference Paper | IST-REx-ID: 3841 | OA
T. A. Henzinger, B. Jobstmann, and V. Wolf, “Formalisms for specifying Markovian population models,” presented at the RP: Reachability Problems, Palaiseau, France, 2009, vol. 5797, pp. 3–23.
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2009 | Conference Paper | IST-REx-ID: 3843 | OA
F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “Fast adaptive uniformization of the chemical master equation,” presented at the HIBI: High-Performance Computational Systems Biology, Trento, Italy, 2009, vol. 4, no. 6, pp. 118–127.
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2009 | Conference Paper | IST-REx-ID: 3844 | OA
T. A. Henzinger, C. Kirsch, E. Marques, and A. Sokolova, “Distributed, modular HTL,” presented at the RTSS: Real-Time Systems Symposium, Washington, DC, United States, 2009, pp. 171–180.
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2009 | Journal Article | IST-REx-ID: 3870 | OA
K. Chatterjee, T. A. Henzinger, and F. Horn, “Finitary winning in omega-regular games,” ACM Transactions on Computational Logic (TOCL), vol. 11, no. 1. ACM, 2009.
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2009 | Conference Paper | IST-REx-ID: 3871 | OA
K. Chatterjee, L. Doyen, and T. A. Henzinger, “Probabilistic weighted automata,” presented at the CONCUR: Concurrency Theory, Bologna, Italy, 2009, vol. 5710, pp. 244–258.
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2009 | Conference Paper | IST-REx-ID: 3968 | OA
H. Edelsbrunner and J. Harer, “The persistent Morse complex segmentation of a 3-manifold,” presented at the 3DPH: Modelling the Physiological Human, Zermatt, Switzerland, 2009, vol. 5903, pp. 36–50.
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2009 | Journal Article | IST-REx-ID: 4136 | OA
J. Polechova, N. H. Barton, and G. Marion, “Species’ range: Adaptation in space and time,” American Naturalist, vol. 174, no. 5. University of Chicago Press, pp. E186–E204, 2009.
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2009 | Journal Article | IST-REx-ID: 4231
N. H. Barton and H. De Vladar, “Statistical mechanics and the evolution of polygenic quantitative traits,” Genetics, vol. 181, no. 3. Genetics Society of America, pp. 997–1011, 2009.
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2009 | Journal Article | IST-REx-ID: 4242 | OA
N. H. Barton and M. De Cara, “The evolution of strong reproductive isolation,” Evolution; International Journal of Organic Evolution, vol. 63, no. 5. Wiley, pp. 1171–1190, 2009.
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2008 | Journal Article | IST-REx-ID: 517
N. H. Barton, “Identity and coalescence in structured populations: A commentary on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin,” Genetical Research, vol. 89, no. 5–6. Cambridge University Press, pp. 475–477, 2008.
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2008 | Journal Article | IST-REx-ID: 9457 | OA
D. Zilberman, D. Coleman-Derr, T. Ballinger, and S. Henikoff, “Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks,” Nature, vol. 456, no. 7218. Springer Nature, pp. 125–129, 2008.
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2008 | Journal Article | IST-REx-ID: 9537
D. Zilberman, “The evolving functions of DNA methylation,” Current Opinion in Plant Biology, vol. 11, no. 5. Elsevier , pp. 554–559, 2008.
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2007 | Journal Article | IST-REx-ID: 9487 | OA
J. Penterman, D. Zilberman, J. H. Huh, T. Ballinger, S. Henikoff, and R. L. Fischer, “DNA demethylation in the Arabidopsis genome,” Proceedings of the National Academy of Sciences, vol. 104, no. 16. National Academy of Sciences, pp. 6752–6757, 2007.
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2007 | Other Publication | IST-REx-ID: 9504
D. Zilberman, The human promoter methylome, vol. 39, no. 4. Nature Publishing Group, 2007, pp. 442–443.
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2007 | Journal Article | IST-REx-ID: 9524 | OA
D. Zilberman and S. Henikoff, “Genome-wide analysis of DNA methylation patterns,” Development, vol. 134, no. 22. The Company of Biologists, pp. 3959–3965, 2007.
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2006 | Journal Article | IST-REx-ID: 9505
D. Zilberman, M. Gehring, R. K. Tran, T. Ballinger, and S. Henikoff, “Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription,” Nature Genetics, vol. 39, no. 1. Nature Publishing Group, pp. 61–69, 2006.
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2005 | Journal Article | IST-REx-ID: 9491 | OA
R. K. Tran, J. G. Henikoff, D. Zilberman, R. F. Ditt, S. E. Jacobsen, and S. Henikoff, “DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes,” Current Biology, vol. 15, no. 2. Elsevier, pp. 154–159, 2005.
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2005 | Journal Article | IST-REx-ID: 9514 | OA
R. K. Tran et al., “Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis,” Genome Biology, vol. 6, no. 11. Springer Nature, 2005.
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2005 | Journal Article | IST-REx-ID: 9529
D. Zilberman and S. Henikoff, “Epigenetic inheritance in Arabidopsis: Selective silence,” Current Opinion in Genetics and Development, vol. 15, no. 5. Elsevier, pp. 557–562, 2005.
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2004 | Journal Article | IST-REx-ID: 9454
S. W.-L. Chan, D. Zilberman, Zhixin Xie, Lisa K. Johansen, J. C. Carrington, and S. E. Jacobsen, “RNA silencing genes control de novo DNA methylation,” Science, vol. 303, no. 5662. American Association for the Advancement of Science, p. 1336, 2004.
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2004 | Journal Article | IST-REx-ID: 9493 | OA
D. Zilberman, X. Cao, L. K. Johansen, Z. Xie, J. C. Carrington, and S. E. Jacobsen, “Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats,” Current Biology, vol. 14, no. 13. Elsevier, pp. 1214–1220, 2004.
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2004 | Journal Article | IST-REx-ID: 9511 | OA
D. Zilberman and S. Henikoff, “Silencing of transposons in plant genomes: kick them when they’re down,” Genome Biology, vol. 5, no. 12. Springer Nature, 2004.
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2004 | Journal Article | IST-REx-ID: 9517 | OA
Z. Xie et al., “Genetic and functional diversification of small RNA pathways in plants,” PLoS Biology, vol. 2, no. 5. Public Library of Science, pp. 0642–0652, 2004.
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2003 | Journal Article | IST-REx-ID: 9455
D. Zilberman, Xiaofeng Cao, and S. E. Jacobsen, “ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation,” Science, vol. 299, no. 5607. American Association for the Advancement of Science, pp. 716–719, 2003.
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2003 | Journal Article | IST-REx-ID: 9495 | OA
X. Cao et al., “Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation,” Current Biology, vol. 13, no. 24. Elsevier, pp. 2212–2217, 2003.
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2001 | Journal Article | IST-REx-ID: 9444
A. M. Lindroth et al., “Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation,” Science, vol. 292, no. 5524. American Association for the Advancement of Science, pp. 2077–2080, 2001.
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