On the application of statistical physics to evolutionary biology
N.H. Barton, J. Coe, Journal of Theoretical Biology 259 (2009) 317–324.
LibreCat: https://research-explorer.ista.ac.at/record/3775
DOI: 10.1016/j.jtbi.2009.03.019

On relational interfaces
S. Tripakis, B. Lickly, T.A. Henzinger, E. Lee, in:, EMSOFT ’09 Proceedings of the Seventh ACM International Conference on Embedded Software, ACM, 2009, pp. 67–76.
LibreCat: https://research-explorer.ista.ac.at/record/3837
DOI: 10.1145/1629335.1629346

The persistent Morse complex segmentation of a 3-manifold
H. Edelsbrunner, J. Harer, in:, Springer, 2009, pp. 36–50.
LibreCat: https://research-explorer.ista.ac.at/record/3968
DOI: 10.1007/978-3-642-10470-1_4

Statistical mechanics and the evolution of polygenic quantitative traits
N.H. Barton, H. De Vladar, Genetics 181 (2009) 997–1011.
LibreCat: https://research-explorer.ista.ac.at/record/4231
DOI: 10.1534/genetics.108.099309

Alternating weighted automata
K. Chatterjee, L. Doyen, T.A. Henzinger, in:, Springer, 2009, pp. 3–13.
LibreCat: https://research-explorer.ista.ac.at/record/4542
DOI: 10.1007/978-3-642-03409-1_2

A survey of stochastic games with limsup and liminf objectives
K. Chatterjee, L. Doyen, T.A. Henzinger, in:, Springer, 2009, pp. 1–15.
LibreCat: https://research-explorer.ista.ac.at/record/4545
DOI: 10.1007/978-3-642-02930-1_1

Stochastic games with finitary objectives
K. Chatterjee, T.A. Henzinger, F. Horn, in:, Springer, 2009, pp. 34–54.
LibreCat: https://research-explorer.ista.ac.at/record/4543
DOI: 10.1007/978-3-642-03816-7_4

Better quality in synthesis through quantitative objectives
R. Bloem, K. Chatterjee, T.A. Henzinger, B. Jobstmann, in:, Springer, 2009, pp. 140–156.
LibreCat: https://research-explorer.ista.ac.at/record/4569
DOI: 10.1007/978-3-642-02658-4_14
arXiv: 0904.2638

Gist: A solver for probabilistic games
K. Chatterjee, T.A. Henzinger, B. Jobstmann, A. Radhakrishna, Gist: A Solver for Probabilistic Games, IST Austria, 2009.
LibreCat: https://research-explorer.ista.ac.at/record/5393
DOI: 10.15479/AT:IST-2009-0003

Improved lower bounds for request-response and finitary Streett games
K. Chatterjee, T.A. Henzinger, F. Horn, Improved Lower Bounds for Request-Response and Finitary Streett Games, IST Austria, 2009.
LibreCat: https://research-explorer.ista.ac.at/record/5394
DOI: 10.15479/AT:IST-2009-0002

Probabilistic automata on infinite words: Decidability and undecidability results
K. Chatterjee, Probabilistic Automata on Infinite Words: Decidability and Undecidability Results, IST Austria, 2009.
LibreCat: https://research-explorer.ista.ac.at/record/5392
DOI: 10.15479/AT:IST-2009-0004

Qualitative analysis of partially-observable Markov decision processes
K. Chatterjee, L. Doyen, T.A. Henzinger, Qualitative Analysis of Partially-Observable Markov Decision Processes, IST Austria, 2009.
LibreCat: https://research-explorer.ista.ac.at/record/5395
DOI: 10.15479/AT:IST-2009-0001

Genome-wide demethylation of Arabidopsis endosperm
T.-F. Hsieh, C.A. Ibarra, P. Silva, A. Zemach, L. Eshed-Williams, R.L. Fischer, D. Zilberman, Science 324 (2009) 1451–1454.
LibreCat: https://research-explorer.ista.ac.at/record/9453
DOI: 10.1126/science.1172417
PMID: 19520962

The evolving functions of DNA methylation
D. Zilberman, Current Opinion in Plant Biology 11 (2008) 554–559.
LibreCat: https://research-explorer.ista.ac.at/record/9537
DOI: 10.1016/j.pbi.2008.07.004
PMID: 18774331

Histone A.Z and DNA methylation are mutually antagonistic chromatin marks
D. Zilberman, D. Coleman-Derr, T. Ballinger, S. Henikoff, Nature 456 (2008) 125–129.
LibreCat: https://research-explorer.ista.ac.at/record/9457
DOI: 10.1038/nature07324
PMID: 18815594

Identity and coalescence in structured populations: A commentary on 'Inbreeding coefficients and coalescence times' by Montgomery Slatkin
N.H. Barton, Genetics Research 89 (2008) 475–477.
LibreCat: https://research-explorer.ista.ac.at/record/517
DOI: 10.1017/S0016672308009683

DNA demethylation in the Arabidopsis genome
J. Penterman, D. Zilberman, J.H. Huh, T. Ballinger, S. Henikoff, R.L. Fischer, Proceedings of the National Academy of Sciences 104 (2007) 6752–6757.
LibreCat: https://research-explorer.ista.ac.at/record/9487
DOI: 10.1073/pnas.0701861104
PMID: 17409185

The human promoter methylome
D. Zilberman, The Human Promoter Methylome, Nature Publishing Group, 2007.
LibreCat: https://research-explorer.ista.ac.at/record/9504
DOI: 10.1038/ng0407-442
PMID: 17392803

Genome-wide analysis of DNA methylation patterns
D. Zilberman, S. Henikoff, Development 134 (2007) 3959–3965.
LibreCat: https://research-explorer.ista.ac.at/record/9524
DOI: 10.1242/dev.001131
PMID: 17928417

Packaging the male germline in plants
X. Feng, H.G. Dickinson, Trends in Genetics 23 (2007) 503–510.
LibreCat: https://research-explorer.ista.ac.at/record/12201
DOI: 10.1016/j.tig.2007.08.005
PMID: 17825943

Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription
D. Zilberman, M. Gehring, R.K. Tran, T. Ballinger, S. Henikoff, Nature Genetics 39 (2006) 61–69.
LibreCat: https://research-explorer.ista.ac.at/record/9505
DOI: 10.1038/ng1929
PMID: 17128275

DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes
R.K. Tran, J.G. Henikoff, D. Zilberman, R.F. Ditt, S.E. Jacobsen, S. Henikoff, Current Biology 15 (2005) 154–159.
LibreCat: https://research-explorer.ista.ac.at/record/9491
DOI: 10.1016/j.cub.2005.01.008
PMID: 15668172 

Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis
R.K. Tran, D. Zilberman, C. de Bustos, R.F. Ditt, J.G. Henikoff, A.M. Lindroth, J. Delrow, T. Boyle, S. Kwong, T.D. Bryson, S.E. Jacobsen, S. Henikoff, Genome Biology 6 (2005).
LibreCat: https://research-explorer.ista.ac.at/record/9514
DOI: 10.1186/gb-2005-6-11-r90
PMID: 16277745

Epigenetic inheritance in Arabidopsis: Selective silence
D. Zilberman, S. Henikoff, Current Opinion in Genetics and Development 15 (2005) 557–562.
LibreCat: https://research-explorer.ista.ac.at/record/9529
DOI: 10.1016/j.gde.2005.07.002
PMID: 16085410

Role of Arabidopsis ARGONAUT in RNA-directed DNA methylation triggered by inverted repeats
D. Zilberman, X. Cao, L.K. Johansen, Z. Xie, J.C. Carrington, S.E. Jacobsen, Current Biology 14 (2004) 1214–1220.
LibreCat: https://research-explorer.ista.ac.at/record/9493
DOI: 10.1016/j.cub.2004.06.055
PMID: 15242620 

Genetic and functional diversification of small RNA pathways in plants
Z. Xie, L.K. Johansen, A.M. Gustafson, K.D. Kasschau, A.D. Lellis, D. Zilberman, S.E. Jacobsen, J.C. Carrington, PLoS Biology 2 (2004) 0642–0652.
LibreCat: https://research-explorer.ista.ac.at/record/9517
DOI: 10.1371/journal.pbio.0020104
PMID: 15024409

Silencing of transposons in plant genomes: kick them when they're down
D. Zilberman, S. Henikoff, Genome Biology 5 (2004).
LibreCat: https://research-explorer.ista.ac.at/record/9511
DOI: 10.1186/gb-2004-5-12-249
PMID: 15575975

RNA silencing genes control de novo DNA methylation
S.W.-L. Chan, D. Zilberman,  Zhixin Xie,  Lisa K. Johansen, J.C. Carrington, S.E. Jacobsen, Science 303 (2004) 1336.
LibreCat: https://research-explorer.ista.ac.at/record/9454
DOI: 10.1126/science.1095989
PMID: 14988555

A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides
Z. Liao, M. Chen, Y. Gong, L. Guo, Q. Tan, X. Feng, X. Sun, F. Tan, K. Tang, DNA Sequence 15 (2004) 153–158.
LibreCat: https://research-explorer.ista.ac.at/record/12203
DOI: 10.1080/10425170410001667348
PMID: 15352294

Role of the DRM and CM methyltransferases in RNA-directed DNA methylation
X. Cao, W. Aufsatz, D. Zilberman, M.F. Mette, M.S. Huang, M. Matzke, S.E. Jacobsen, Current Biology 13 (2003) 2212–2217.
LibreCat: https://research-explorer.ista.ac.at/record/9495
DOI: 10.1016/j.cub.2003.11.052
PMID: 14680640

ARGONAUT control of locus-specific siRNA accumulation and DNA and histone methylation
D. Zilberman,  Xiaofeng Cao, S.E. Jacobsen, Science 299 (2003) 716–719.
LibreCat: https://research-explorer.ista.ac.at/record/9455
DOI: 10.1126/science.1079695
PMID: 12522258

Requirement of CHROMOMETHYLAS for maintenance of CpXpG methylation
A.M. Lindroth, X. Cao, J.P. Jackson, D. Zilberman, C.M. McCallum, S. Henikoff, S.E. Jacobsen, Science 292 (2001) 2077–2080.
LibreCat: https://research-explorer.ista.ac.at/record/9444
DOI: 10.1126/science.1059745
PMID: 11349138