Henzinger, Thomas A, Barbara Jobstmann, and Verena Wolf. “Formalisms for Specifying Markovian Population Models,”https://doi.org/10.1007/978-3-642-04420-5_2__5797:3–23. Springer, 2009.https://doi.org/10.1007/978-3-642-04420-5_2 .

Henzinger, Thomas A, Christoph Kirsch, Eduardo Marques, and Ana Sokolova. “Distributed, Modular HTL,”https://doi.org/10.1109/RTSS.2009.9__171–80. IEEE, 2009.https://doi.org/10.1109/RTSS.2009.9 .

Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “Probabilistic Weighted Automata,”https://doi.org/10.1007/978-3-642-04081-8_17__5710:244–58. Springer, 2009.https://doi.org/10.1007/978-3-642-04081-8_17 .

Chatterjee, Krishnendu, Thomas A Henzinger, and Florian Horn. “Finitary Winning in Omega-Regular Games.”https://doi.org/10.1145/1614431.1614432__ACM Transactions on Computational Logic (TOCL). ACM, 2009.https://doi.org/10.1145/1614431.1614432 .

Polechova, Jitka, Nicholas H Barton, and Glenn Marion. “Species’ Range: Adaptation in Space and Time.”https://doi.org/10.1086/605958__American Naturalist. University of Chicago Press, 2009.https://doi.org/10.1086/605958 .

Barton, Nicholas H, and Maria De Cara. “The Evolution of Strong Reproductive Isolation.”https://doi.org/10.1111/j.1558-5646.2009.00622.x__Evolution; International Journal of Organic Evolution. Wiley, 2009.https://doi.org/10.1111/j.1558-5646.2009.00622.x .

Barton, Nicholas H. “Why Sex and Recombination? .”https://doi.org/10.1101/sqb.2009.74.030__In Cold Spring Harbor Symposia on Quantitative Biology, 74:187–95. Cold Spring Harbor Laboratory Press, 2009.https://doi.org/10.1101/sqb.2009.74.030 .

Barton, Nicholas H, and Jason Coe. “On the Application of Statistical Physics to Evolutionary Biology.”https://doi.org/10.1016/j.jtbi.2009.03.019__Journal of Theoretical Biology. Elsevier, 2009.https://doi.org/10.1016/j.jtbi.2009.03.019 .

Tripakis, Stavros, Ben Lickly, Thomas A Henzinger, and Edward Lee. “On Relational Interfaces.”https://doi.org/10.1145/1629335.1629346__In EMSOFT ’09 Proceedings of the Seventh ACM International Conference on Embedded Software, 67–76. ACM, 2009.https://doi.org/10.1145/1629335.1629346 .

Edelsbrunner, Herbert, and John Harer. “The Persistent Morse Complex Segmentation of a 3-Manifold,”https://doi.org/10.1007/978-3-642-10470-1_4__5903:36–50. Springer, 2009.https://doi.org/10.1007/978-3-642-10470-1_4 .

Barton, Nicholas H, and Harold De Vladar. “Statistical Mechanics and the Evolution of Polygenic Quantitative Traits.”https://doi.org/10.1534/genetics.108.099309__Genetics. Genetics Society of America, 2009.https://doi.org/10.1534/genetics.108.099309 .

Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “Alternating Weighted Automata,”https://doi.org/10.1007/978-3-642-03409-1_2__5699:3–13. Springer, 2009.https://doi.org/10.1007/978-3-642-03409-1_2 .

Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “A Survey of Stochastic Games with Limsup and Liminf Objectives,”https://doi.org/10.1007/978-3-642-02930-1_1__5556:1–15. Springer, 2009.https://doi.org/10.1007/978-3-642-02930-1_1 .

Chatterjee, Krishnendu, Thomas A Henzinger, and Florian Horn. “Stochastic Games with Finitary Objectives,”https://doi.org/10.1007/978-3-642-03816-7_4__5734:34–54. Springer, 2009.https://doi.org/10.1007/978-3-642-03816-7_4 .

Bloem, Roderick, Krishnendu Chatterjee, Thomas A Henzinger, and Barbara Jobstmann. “Better Quality in Synthesis through Quantitative Objectives,”https://doi.org/10.1007/978-3-642-02658-4_14__5643:140–56. Springer, 2009.https://doi.org/10.1007/978-3-642-02658-4_14 .

Chatterjee, Krishnendu, Thomas A Henzinger, Barbara Jobstmann, and Arjun Radhakrishna. Gist: A Solver for Probabilistic Games. IST Austria, 2009.https://doi.org/10.15479/AT:IST-2009-0003 .

Chatterjee, Krishnendu, Thomas A Henzinger, and Florian Horn. Improved Lower Bounds for Request-Response and Finitary Streett Games. IST Austria, 2009.https://doi.org/10.15479/AT:IST-2009-0002 .

Chatterjee, Krishnendu. Probabilistic Automata on Infinite Words: Decidability and Undecidability Results. IST Austria, 2009.https://doi.org/10.15479/AT:IST-2009-0004 .

Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. Qualitative Analysis of Partially-Observable Markov Decision Processes. IST Austria, 2009.https://doi.org/10.15479/AT:IST-2009-0001 .

Hsieh, Tzung-Fu, Christian A. Ibarra, Pedro Silva, Assaf Zemach, Leor Eshed-Williams, Robert L. Fischer, and Daniel Zilberman. “Genome-Wide Demethylation of Arabidopsis Endosperm.”https://doi.org/10.1126/science.1172417__Science. American Association for the Advancement of Science, 2009.https://doi.org/10.1126/science.1172417 .

Zilberman, Daniel. “The Evolving Functions of DNA Methylation.”https://doi.org/10.1016/j.pbi.2008.07.004__Current Opinion in Plant Biology. Elsevier , 2008.https://doi.org/10.1016/j.pbi.2008.07.004 .

Zilberman, Daniel, Devin Coleman-Derr, Tracy Ballinger, and Steven Henikoff. “Histone A.Z and DNA Methylation Are Mutually Antagonistic Chromatin Marks.”https://doi.org/10.1038/nature07324__Nature. Springer Nature, 2008.https://doi.org/10.1038/nature07324 .

Barton, Nicholas H. “Identity and Coalescence in Structured Populations: A Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery Slatkin.”https://doi.org/10.1017/S0016672308009683__Genetics Research. Cambridge University Press, 2008.https://doi.org/10.1017/S0016672308009683 .

Penterman, Jon, Daniel Zilberman, Jin Hoe Huh, Tracy Ballinger, Steven Henikoff, and Robert L. Fischer. “DNA Demethylation in the Arabidopsis Genome.”https://doi.org/10.1073/pnas.0701861104__Proceedings of the National Academy of Sciences. National Academy of Sciences, 2007.https://doi.org/10.1073/pnas.0701861104 .

Zilberman, Daniel. The Human Promoter Methylome. Nature Genetics. Vol. 39. Nature Publishing Group, 2007.https://doi.org/10.1038/ng0407-442 .

Zilberman, Daniel, and Steven Henikoff. “Genome-Wide Analysis of DNA Methylation Patterns.”https://doi.org/10.1242/dev.001131__Development. The Company of Biologists, 2007.https://doi.org/10.1242/dev.001131 .

Feng, Xiaoqi, and Hugh G. Dickinson. “Packaging the Male Germline in Plants.”https://doi.org/10.1016/j.tig.2007.08.005__Trends in Genetics. Elsevier BV, 2007.https://doi.org/10.1016/j.tig.2007.08.005 .

Zilberman, Daniel, Mary Gehring, Robert K. Tran, Tracy Ballinger, and Steven Henikoff. “Genome-Wide Analysis of Arabidopsis Thaliana DNA Methylation Uncovers an Interdependence between Methylation and Transcription.”https://doi.org/10.1038/ng1929__Nature Genetics. Nature Publishing Group, 2006.https://doi.org/10.1038/ng1929 .

Tran, Robert K., Jorja G. Henikoff, Daniel Zilberman, Renata F. Ditt, Steven E. Jacobsen, and Steven Henikoff. “DNA Methylation Profiling Identifies CG Methylation Clusters in Arabidopsis Genes.”https://doi.org/10.1016/j.cub.2005.01.008__Current Biology. Elsevier, 2005.https://doi.org/10.1016/j.cub.2005.01.008 .

Tran, Robert K., Daniel Zilberman, Cecilia de Bustos, Renata F. Ditt, Jorja G. Henikoff, Anders M. Lindroth, Jeffrey Delrow, et al. “Chromatin and SiRNA Pathways Cooperate to Maintain DNA Methylation of Small Transposable Elements in Arabidopsis.”https://doi.org/10.1186/gb-2005-6-11-r90__Genome Biology. Springer Nature, 2005.https://doi.org/10.1186/gb-2005-6-11-r90 .

Zilberman, Daniel, and Steven Henikoff. “Epigenetic Inheritance in Arabidopsis: Selective Silence.”https://doi.org/10.1016/j.gde.2005.07.002__Current Opinion in Genetics and Development. Elsevier, 2005.https://doi.org/10.1016/j.gde.2005.07.002 .

Zilberman, Daniel, Xiaofeng Cao, Lisa K. Johansen, Zhixin Xie, James C. Carrington, and Steven E. Jacobsen. “Role of Arabidopsis ARGONAUT in RNA-Directed DNA Methylation Triggered by Inverted Repeats.”https://doi.org/10.1016/j.cub.2004.06.055__Current Biology. Elsevier, 2004.https://doi.org/10.1016/j.cub.2004.06.055 .

Xie, Zhixin, Lisa K. Johansen, Adam M. Gustafson, Kristin D. Kasschau, Andrew D.https://doi.org/10.1371/journal.pbio.0020104__Lellis, Daniel Zilberman, Steven E. Jacobsen, and James C. Carrington. “Genetic and Functional Diversification of Small RNA Pathways in Plants.”https://doi.org/10.1371/journal.pbio.0020104__PLoS Biology. Public Library of Science, 2004.https://doi.org/10.1371/journal.pbio.0020104 .

Zilberman, Daniel, and Steven Henikoff. “Silencing of Transposons in Plant Genomes: Kick Them When They’re Down.”https://doi.org/10.1186/gb-2004-5-12-249__Genome Biology. Springer Nature, 2004.https://doi.org/10.1186/gb-2004-5-12-249 .

Chan, Simon W.-L., Daniel Zilberman,https://doi.org/10.1126/science.1095989__Zhixin Xie,https://doi.org/10.1126/science.1095989__Lisa K. Johansen, James C. Carrington, and Steven E. Jacobsen. “RNA Silencing Genes Control de Novo DNA Methylation.”https://doi.org/10.1126/science.1095989__Science. American Association for the Advancement of Science, 2004.https://doi.org/10.1126/science.1095989 .

Liao, Zhihua, Min Chen, Yifu Gong, Liang Guo, Qiumin Tan, Xiaoqi Feng, Xiaofen Sun, Feng Tan, and Kexuan Tang. “A New Geranylgeranyl Diphosphate Synthase Gene from Ginkgo Biloba, Which Intermediates the Biosynthesis of the Key Precursor for Ginkgolides.”https://doi.org/10.1080/10425170410001667348__DNA Sequence. Informa UK Limited, 2004.https://doi.org/10.1080/10425170410001667348 .

Cao, Xiaofeng, Werner Aufsatz, Daniel Zilberman, M.Florian Mette, Michael S. Huang, Marjori Matzke, and Steven E. Jacobsen. “Role of the DRM and CM Methyltransferases in RNA-Directed DNA Methylation.”https://doi.org/10.1016/j.cub.2003.11.052__Current Biology. Elsevier, 2003.https://doi.org/10.1016/j.cub.2003.11.052 .

Zilberman, Daniel,https://doi.org/10.1126/science.1079695__Xiaofeng Cao, and Steven E. Jacobsen. “ARGONAUT Control of Locus-Specific SiRNA Accumulation and DNA and Histone Methylation.”https://doi.org/10.1126/science.1079695__Science. American Association for the Advancement of Science, 2003.https://doi.org/10.1126/science.1079695 .

Lindroth, A. M., Xiaofeng Cao, James P. Jackson, Daniel Zilberman, Claire M. McCallum, Steven Henikoff, and Steven E. Jacobsen. “Requirement of CHROMOMETHYLAS for Maintenance of CpXpG Methylation.”https://doi.org/10.1126/science.1059745__Science. American Association for the Advancement of Science, 2001.https://doi.org/10.1126/science.1059745 .