Davison A, Barton NH, Clarke B. 2009. 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. 22(8), 1624–1635.

Didier F, Henzinger TA, Mateescu M, Wolf V. 2009. Fast adaptive uniformization of the chemical master equation. HIBI: High-Performance Computational Systems Biology vol. 4, 118–127.

Henzinger TA, Jobstmann B, Wolf V. 2009. Formalisms for specifying Markovian population models. RP: Reachability Problems, LNCS, vol. 5797, 3–23.

Henzinger TA, Kirsch C, Marques E, Sokolova A. 2009. Distributed, modular HTL. RTSS: Real-Time Systems Symposium, 171–180.

Chatterjee K, Doyen L, Henzinger TA. 2009. Probabilistic weighted automata. CONCUR: Concurrency Theory, LNCS, vol. 5710, 244–258.

Chatterjee K, Henzinger TA, Horn F. 2009. Finitary winning in omega-regular games. ACM Transactions on Computational Logic (TOCL). 11(1), 1.

Polechova J, Barton NH, Marion G. 2009. Species’ range: Adaptation in space and time. American Naturalist. 174(5), 6–4.

Barton NH, De Cara M. 2009. The evolution of strong reproductive isolation. Evolution; International Journal of Organic Evolution. 63(5), 1171–1190.

Barton NH. 2009.Why sex and recombination? . In: Cold Spring Harbor Symposia on Quantitative Biology. vol. 74, 187–195.

Barton NH, Coe J. 2009. On the application of statistical physics to evolutionary biology. Journal of Theoretical Biology. 259(2), 317–324.

Tripakis S, Lickly B, Henzinger TA, Lee E. 2009. On relational interfaces. EMSOFT ’09 Proceedings of the seventh ACM international conference on Embedded software. EMSOFT: Embedded Software , 67–76.

Edelsbrunner H, Harer J. 2009. The persistent Morse complex segmentation of a 3-manifold. 3DPH: Modelling the Physiological Human, LNCS, vol. 5903, 36–50.

Barton NH, De Vladar H. 2009. Statistical mechanics and the evolution of polygenic quantitative traits. Genetics. 181(3), 997–1011.

Chatterjee K, Doyen L, Henzinger TA. 2009. Alternating weighted automata. FCT: Fundamentals of Computation Theory, LNCS, vol. 5699, 3–13.

Chatterjee K, Doyen L, Henzinger TA. 2009. A survey of stochastic games with limsup and liminf objectives. ICALP: Automata, Languages and Programming, LNCS, vol. 5556, 1–15.

Chatterjee K, Henzinger TA, Horn F. 2009. Stochastic games with finitary objectives. MFCS: Mathematical Foundations of Computer Science, LNCS, vol. 5734, 34–54.

Bloem R, Chatterjee K, Henzinger TA, Jobstmann B. 2009. Better quality in synthesis through quantitative objectives. CAV: Computer Aided Verification, LNCS, vol. 5643, 140–156.

Chatterjee K, Henzinger TA, Jobstmann B, Radhakrishna A. 2009. Gist: A solver for probabilistic games, IST Austria, 12p.

Chatterjee K, Henzinger TA, Horn F. 2009. Improved lower bounds for request-response and finitary Streett games, IST Austria, 11p.

Chatterjee K. 2009. Probabilistic automata on infinite words: Decidability and undecidability results, IST Austria, 17p.

Chatterjee K, Doyen L, Henzinger TA. 2009. Qualitative analysis of partially-observable Markov decision processes, IST Austria, 20p.

Hsieh T-F, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, Fischer RL, Zilberman D. 2009. Genome-wide demethylation of Arabidopsis endosperm. Science. 324(5933), 1451–1454.

Zilberman D. 2008. The evolving functions of DNA methylation. Current Opinion in Plant Biology. 11(5), 554–559.

Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. 2008. Histone A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature. 456(7218), 125–129.

Barton NH. 2008. Identity and coalescence in structured populations: A commentary on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin. Genetics Research. 89(5–6), 475–477.

Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL. 2007. DNA demethylation in the Arabidopsis genome. Proceedings of the National Academy of Sciences. 104(16), 6752–6757.

Zilberman D. 2007. The human promoter methylome, Nature Publishing Group,p.

Zilberman D, Henikoff S. 2007. Genome-wide analysis of DNA methylation patterns. Development. 134(22), 3959–3965.

Feng X, Dickinson HG. 2007. Packaging the male germline in plants. Trends in Genetics. 23(10), 503–510.

Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. 2006. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nature Genetics. 39(1), 61–69.

Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S. 2005. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Current Biology. 15(2), 154–159.

Tran RK, Zilberman D, de Bustos C, Ditt RF, Henikoff JG, Lindroth AM, Delrow J, Boyle T, Kwong S, Bryson TD, Jacobsen SE, Henikoff S. 2005. Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biology. 6(11), .

Zilberman D, Henikoff S. 2005. Epigenetic inheritance in Arabidopsis: Selective silence. Current Opinion in Genetics and Development. 15(5), 557–562.

Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. 2004. Role of Arabidopsis ARGONAUT in RNA-directed DNA methylation triggered by inverted repeats. Current Biology. 14(13), 1214–1220.

Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC. 2004. Genetic and functional diversification of small RNA pathways in plants. PLoS Biology. 2(5), 0642–0652.

Zilberman D, Henikoff S. 2004. Silencing of transposons in plant genomes: kick them when they’re down. Genome Biology. 5(12), 249.

Chan SW-L, Zilberman D, Xie  Zhixin, Johansen  Lisa K., Carrington JC, Jacobsen SE. 2004. RNA silencing genes control de novo DNA methylation. Science. 303(5662), 1336.

Liao Z, Chen M, Gong Y, Guo L, Tan Q, Feng X, Sun X, Tan F, Tang K. 2004. A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides. DNA Sequence. 15(2), 153–158.

Cao X, Aufsatz W, Zilberman D, Mette MF, Huang MS, Matzke M, Jacobsen SE. 2003. Role of the DRM and CM methyltransferases in RNA-directed DNA methylation. Current Biology. 13(24), 2212–2217.

Zilberman D, Cao  Xiaofeng, Jacobsen SE. 2003. ARGONAUT control of locus-specific siRNA accumulation and DNA and histone methylation. Science. 299(5607), 716–719.

Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE. 2001. Requirement of CHROMOMETHYLAS for maintenance of CpXpG methylation. Science. 292(5524), 2077–2080.