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.

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.

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.

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.

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. 6–4, 2009.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

K. Chatterjee, T. A. Henzinger, B. Jobstmann, and A. Radhakrishna, Gist: A solver for probabilistic games. IST Austria, 2009.

K. Chatterjee, T. A. Henzinger, and F. Horn, Improved lower bounds for request-response and finitary Streett games. IST Austria, 2009.

K. Chatterjee, Probabilistic automata on infinite words: Decidability and undecidability results. IST Austria, 2009.

K. Chatterjee, L. Doyen, and T. A. Henzinger, Qualitative analysis of partially-observable Markov decision processes. IST Austria, 2009.

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.

D. Zilberman, “The evolving functions of DNA methylation,” Current Opinion in Plant Biology, vol. 11, no. 5. Elsevier , pp. 554–559, 2008.

D. Zilberman, D. Coleman-Derr, T. Ballinger, and S. Henikoff, “Histone A.Z and DNA methylation are mutually antagonistic chromatin marks,” Nature, vol. 456, no. 7218. Springer Nature, pp. 125–129, 2008.

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.

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.

D. Zilberman, The human promoter methylome, vol. 39, no. 4. Nature Publishing Group, 2007, pp. 442–443.

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.

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.

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.

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.

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.

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.

D. Zilberman, X. Cao, L. K. Johansen, Z. Xie, J. C. Carrington, and S. E. Jacobsen, “Role of Arabidopsis ARGONAUT in RNA-directed DNA methylation triggered by inverted repeats,” Current Biology, vol. 14, no. 13. Elsevier, pp. 1214–1220, 2004.

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.

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.

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.

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.

X. Cao et al., “Role of the DRM and CM methyltransferases in RNA-directed DNA methylation,” Current Biology, vol. 13, no. 24. Elsevier, pp. 2212–2217, 2003.

D. Zilberman,  Xiaofeng Cao, and S. E. Jacobsen, “ARGONAUT 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.

A. M. Lindroth et al., “Requirement of CHROMOMETHYLAS for maintenance of CpXpG methylation,” Science, vol. 292, no. 5524. American Association for the Advancement of Science, pp. 2077–2080, 2001.