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4969 Publications

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: 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.
[Submitted Version] View | Files available | DOI
 
2010 | Journal Article | IST-REx-ID: 3867 | OA
K. Chatterjee, L. Doyen, and T. A. Henzinger, “Expressiveness and closure properties for quantitative languages,” Logical Methods in Computer Science, vol. 6, no. 3. International Federation of Computational Logic, pp. 1–23, 2010.
[Published Version] View | Files available | DOI
 
2010 | Journal Article | IST-REx-ID: 474
N. H. Barton, J. Kelleher, and A. Etheridge, “A new model for extinction and recolonization in two dimensions: Quantifying phylogeography,” Evolution, vol. 64, no. 9. Wiley-Blackwell, pp. 2701–2715, 2010.
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2010 | Conference Paper | IST-REx-ID: 488 | OA
R. Alur and P. Cerny, “Expressiveness of streaming string transducers,” presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, Chennai, India, 2010, vol. 8, pp. 1–12.
[Published Version] View | Files available | DOI
 
2010 | Conference Paper | IST-REx-ID: 489 | OA
J. Cristau, C. David, and F. Horn, “How do we remember the past in randomised strategies? ,” in Proceedings of GandALF 2010, Minori, Amalfi Coast, Italy, 2010, vol. 25, pp. 30–39.
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2010 | Journal Article | IST-REx-ID: 533
J. Hoenicke, K. Leino, A. Podelski, M. Schäf, and T. Wies, “Doomed program points,” Formal Methods in System Design, vol. 37, no. 2–3. Springer, pp. 171–199, 2010.
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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.
[Submitted Version] View | Files available | DOI
 
2010 | Technical Report | IST-REx-ID: 5388 | OA
K. Chatterjee, P. Cerny, T. A. Henzinger, A. Radhakrishna, and R. Singh, Quantitative synthesis for concurrent programs. IST Austria, 2010.
[Published Version] View | Files available | DOI
 
2010 | Technical Report | IST-REx-ID: 5389 | OA
P. Cerny, T. A. Henzinger, and A. Radhakrishna, Simulation distances. IST Austria, 2010.
[Published Version] View | Files available | DOI
 
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.
[Submitted Version] View | Files available | DOI
 
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.
[Submitted Version] View | Files available | DOI | arXiv
 
2010 | Technical Report | IST-REx-ID: 5391 | OA
P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, and R. Alur, Model checking of linearizability of concurrent list implementations. IST Austria, 2010.
[Published Version] View | Files available | DOI
 
2010 | Technical Report | IST-REx-ID: 5390 | OA
K. Chatterjee and N. Fijalkow, Topological, automata-theoretic and logical characterization of finitary languages. IST Austria, 2010.
[Published Version] View | Files available | DOI
 
2010 | Conference Paper | IST-REx-ID: 3857
K. Chatterjee and T. A. Henzinger, “Probabilistic Automata on infinite words: decidability and undecidability results,” presented at the ATVA: Automated Technology for Verification and Analysis, Singapore, Singapore, 2010, vol. 6252, pp. 1–16.
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2010 | Conference Paper | IST-REx-ID: 3855 | OA
K. Chatterjee, L. Doyen, and T. A. Henzinger, “Qualitative analysis of partially-observable Markov Decision Processes,” presented at the MFCS: Mathematical Foundations of Computer Science, Brno, Czech Republic, 2010, vol. 6281, pp. 258–269.
[Submitted Version] View | Files available | DOI
 
2010 | Journal Article | IST-REx-ID: 9485 | OA
A. Zemach et al., “Local DNA hypomethylation activates genes in rice endosperm,” Proceedings of the National Academy of Sciences, vol. 107, no. 43. National Academy of Sciences, pp. 18729–18734, 2010.
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2010 | Journal Article | IST-REx-ID: 9489 | OA
A. Zemach and D. Zilberman, “Evolution of eukaryotic DNA methylation and the pursuit of safer sex,” Current Biology, vol. 20, no. 17. Elsevier, pp. R780–R785, 2010.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
2010 | Journal Article | IST-REx-ID: 9452
A. Zemach, I. E. McDaniel, P. Silva, and D. Zilberman, “Genome-wide evolutionary analysis of eukaryotic DNA methylation,” Science, vol. 328, no. 5980. American Association for the Advancement of Science, pp. 916–919, 2010.
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2010 | Journal Article | IST-REx-ID: 3779 | OA
U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Cryptic variation between species and the basis of hybrid performance,” PLoS Biology, vol. 8, no. 7. Public Library of Science, 2010.
[Published Version] View | Files available | DOI
 
2010 | Research Data Reference | IST-REx-ID: 9764
U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Heterosis and the drift load.” Public Library of Science, 2010.
[Published Version] View | Files available | DOI
 
2010 | Journal Article | IST-REx-ID: 12199
X. Feng and H. G. Dickinson, “Tapetal cell fate, lineage and proliferation in the Arabidopsis anther,” Development, vol. 137, no. 14. The Company of Biologists, pp. 2409–2416, 2010.
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2010 | Journal Article | IST-REx-ID: 12200
X. Feng and H. G. Dickinson, “Cell–cell interactions during patterning of the Arabidopsis anther,” Biochemical Society Transactions, vol. 38, no. 2. Portland Press Ltd., pp. 571–576, 2010.
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2010 | Conference Paper | IST-REx-ID: 3852 | OA
K. Chatterjee and R. Majumdar, “Discounting in games across time scales,” presented at the GandALF: Games, Automata, Logic, and Formal Verification, Minori, Italy, 2010, vol. 25, pp. 22–29.
[Published Version] View | Files available | DOI | arXiv
 
2010 | Thesis | IST-REx-ID: 3962
H. Pflicke, “  Dendritic cell migration across basement membranes in the skin,” Institute of Science and Technology Austria, 2010.
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2010 | Conference Paper | IST-REx-ID: 4361 | OA
T. Wies, D. Zufferey, and T. A. Henzinger, “Forward analysis of depth-bounded processes,” presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Paphos, Cyprus, 2010, vol. 6014, pp. 94–108.
[Submitted Version] View | Files available | DOI
 
2010 | Journal Article | IST-REx-ID: 3785
F. Palero, P. Abello, E. Macpherson, C. Matthee, and M. Pascual, “Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata),” Journal of Crustacean Biology, vol. 30, no. 4. Oxford University Press, pp. 658–663, 2010.
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2010 | Book Chapter | IST-REx-ID: 14983
A. Schlögl, C. Vidaurre, and K.-R. Müller, “Adaptive Methods in BCI Research - An Introductory Tutorial,” in Brain-Computer Interfaces, 1st ed., B. Graimann, G. Pfurtscheller, and B. Allison, Eds. Berlin, Heidelberg: Springer, 2010, pp. 331–355.
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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.
[Submitted Version] View | Files available | DOI
 
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.
[Submitted Version] View | Files available | DOI
 
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.
[Submitted Version] View | Files available | DOI
 
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.
[Submitted Version] View | Files available | DOI
 
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.
[Submitted Version] View | Files available | DOI
 
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.
[Submitted Version] View | Files available | DOI
 
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.
[Published Version] View | Files available | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
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.
[Submitted Version] View | Files available | DOI
 
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 | 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.
[Submitted Version] View | Files available | DOI
 
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.
[Submitted Version] View | Files available | DOI
 
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 | 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.
[Submitted Version] View | Files available | DOI
 
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.
[Submitted Version] View | Files available | DOI
 
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: 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.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
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.
[Published Version] View | Files available | DOI
 
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.
[Published Version] View | Files available | DOI
 
2009 | Technical Report | IST-REx-ID: 5392 | OA
K. Chatterjee, Probabilistic automata on infinite words: Decidability and undecidability results. IST Austria, 2009.
[Published Version] View | Files available | DOI
 
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.
[Published Version] View | Files available | DOI
 
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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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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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: 517
N. H. Barton, “Identity and coalescence in structured populations: A commentary on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin,” Genetics Research, vol. 89, no. 5–6. Cambridge University Press, pp. 475–477, 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.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
2007 | Journal Article | IST-REx-ID: 12201
X. Feng and H. G. Dickinson, “Packaging the male germline in plants,” Trends in Genetics, vol. 23, no. 10. Elsevier BV, pp. 503–510, 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.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
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.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
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: 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.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
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.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
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.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
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: 12203
Z. Liao et al., “A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides,” DNA Sequence, vol. 15, no. 2. Informa UK Limited, pp. 153–158, 2004.
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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.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
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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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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