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147 Publications


2005 | Journal Article | IST-REx-ID: 3933
M. K. Sixt et al., “The conduit system transports soluble antigens from the afferent lymph to resident dendritic cells in the T cell area of the lymph node,” Immunity, vol. 22, no. 1. Cell Press, pp. 19–29, 2005.
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2005 | Journal Article | IST-REx-ID: 3983
J. Sohn et al., “Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate,” Biochemistry, vol. 44, no. 50. ACS, pp. 16563–16573, 2005.
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2005 | Conference Paper | IST-REx-ID: 3982
Y. Wang, P. Agarwal, P. Brown, H. Edelsbrunner, and J. Rudolph, “Coarse and reliable geometric alignment for protein docking,” presented at the PSB: Pacific Symposium on Biocomputing, 2005, pp. 64–75.
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2005 | Journal Article | IST-REx-ID: 4144
F. Ulrich et al., “Wnt11 functions in gastrulation by controlling cell cohesion through Rab5c and E-cadherin,” Developmental Cell, vol. 9, no. 4. Cell Press, pp. 555–564, 2005.
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2005 | Journal Article | IST-REx-ID: 4138
N. H. Barton and J. Polechova, “The limitations of adaptive dynamics as a model of evolution,” Journal of Evolutionary Biology, vol. 18, no. 5. Wiley-Blackwell, pp. 1186–1190, 2005.
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2005 | Journal Article | IST-REx-ID: 4155
P. Puech, A. Taubenberger, F. Ulrich, M. Krieg, D. Mueller, and C.-P. J. Heisenberg, “Measuring cell adhesion forces of primary gastrulating cells from zebrafish using atomic force microscopy,” Journal of Cell Science, vol. 118, no. 18. Company of Biologists, pp. 4199–4206, 2005.
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2005 | Journal Article | IST-REx-ID: 4171
J. Montero, L. Carvalho, M. Wilsch Bräuninger, B. Kilian, C. Mustafa, and C.-P. J. Heisenberg, “Shield formation at the onset of zebrafish gastrulation,” Development, vol. 132, no. 6. Company of Biologists, pp. 1187–1198, 2005.
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2005 | Journal Article | IST-REx-ID: 4249
J. Polechova and N. H. Barton, “Speciation through competition: A critical review,” Evolution; International Journal of Organic Evolution, vol. 59, no. 6. Wiley-Blackwell, pp. 1194–1210, 2005.
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2005 | Journal Article | IST-REx-ID: 4251
N. H. Barton and S. Otto, “Evolution of recombination due to random drift,” Genetics, vol. 169, no. 4. Genetics Society of America, pp. 2353–2370, 2005.
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2005 | Journal Article | IST-REx-ID: 4252 | OA
T. Johnson and N. H. Barton, “Theoretical models of selection and mutationon quantitative traits,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 360, no. 1459. Royal Society, The, pp. 1411–1425, 2005.
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2005 | Conference Paper | IST-REx-ID: 4404
R. Alur, P. Cerny, P. Madhusudan, and W. Nam, “Synthesis of interface specifications for Java classes,” presented at the POPL: Principles of Programming Languages, 2005, pp. 98–109.
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2005 | Conference Paper | IST-REx-ID: 4412
S. Matic and T. A. Henzinger, “Trading end-to-end latency for composability,” presented at the RTSS: Real-Time Systems Symposium, 2005, pp. 99–110.
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2005 | Conference Paper | IST-REx-ID: 4418
C. Kirsch, M. Sanvido, and T. A. Henzinger, “A programmable microkernel for real-time systems,” presented at the VEE: Virtual Execution Environments, 2005, pp. 35–45.
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2005 | Journal Article | IST-REx-ID: 4454
T. A. Henzinger, R. Majumdar, and J. Raskin, “A classification of symbolic transition systems,” ACM Transactions on Computational Logic (TOCL), vol. 6, no. 1. ACM, pp. 1–32, 2005.
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2005 | Conference Paper | IST-REx-ID: 4455
T. A. Henzinger, R. Majumdar, and V. Prabhu, “Quantifying similarities between timed systems,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2005, vol. 3829, pp. 226–241.
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2005 | Conference Paper | IST-REx-ID: 4456
T. A. Henzinger, R. Jhala, and R. Majumdar, “Permissive interfaces,” presented at the FSE: Foundations of Software Engineering, 2005, pp. 31–40.
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2005 | Conference Paper | IST-REx-ID: 4457
T. A. Henzinger, C. Kirsch, and S. Matic, “Composable code generation for distributed Giotto,” presented at the LCTES: Languages, Compilers, and Tools for Embedded Systems, 2005, pp. 21–30.
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2005 | Conference Paper | IST-REx-ID: 4536
L. Doyen, T. A. Henzinger, and J. Raskin, “Automatic rectangular refinement of affine hybrid systems,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2005, vol. 3829, pp. 144–161.
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2005 | Conference Paper | IST-REx-ID: 4541
K. Chatterjee and T. A. Henzinger, “Semiperfect-information games,” presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, 2005, vol. 3821, pp. 1–18.
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2005 | Conference Paper | IST-REx-ID: 4553
K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “The complexity of stochastic Rabin and Streett games,” presented at the ICALP: Automata, Languages and Programming, 2005, vol. 3580, pp. 878–890.
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2005 | Conference Paper | IST-REx-ID: 4554
K. Chatterjee, T. A. Henzinger, and M. Jurdziński, “Mean-payoff parity games,” presented at the LICS: Logic in Computer Science, 2005, pp. 178–187.
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2005 | Conference Paper | IST-REx-ID: 4560
A. Chakrabarti, K. Chatterjee, T. A. Henzinger, O. Kupferman, and R. Majumdar, “Verifying quantitative properties using bound functions,” presented at the CHARME: Correct Hardware Design and Verification Methods, 2005, vol. 3725, pp. 50–64.
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2005 | Conference Paper | IST-REx-ID: 4557
K. Chatterjee, T. A. Henzinger, R. Jhala, and R. Majumdar, “Counterexample-guided planning,” presented at the UAI: Uncertainty in Artificial Intelligence, 2005, pp. 104–111.
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2005 | Conference Paper | IST-REx-ID: 4579
D. Beyer, T. A. Henzinger, R. Jhala, and R. Majumdar, “Checking memory safety with BLAST,” presented at the FASE: Fundamental Approaches To Software Engineering, 2005, vol. 3442, pp. 2–18.
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2005 | Conference Paper | IST-REx-ID: 4576
D. Beyer, A. Chakrabarti, and T. A. Henzinger, “Web service interfaces,” presented at the WWW: World Wide Web Conference, 2005, pp. 148–159.
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2005 | Journal Article | IST-REx-ID: 4625
L. De Alfaro, M. Faella, T. A. Henzinger, R. Majumdar, and M. Stoelinga, “Model checking discounted temporal properties,” Theoretical Computer Science, vol. 345, no. 1. Elsevier, pp. 139–170, 2005.
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2005 | Conference Paper | IST-REx-ID: 4624
L. De Alfaro and T. A. Henzinger, “Interface-based design,” presented at the Engineering Theories of Software Intensive Systems, 2005, vol. 195, pp. 83–104.
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2005 | Conference Paper | IST-REx-ID: 575
O. Hosten, M. Rakher, J. Barreiro, N. Peters, and P. Kwiat, “Counterfactual quantum computation,” presented at the QELS: Quantum Electronics and Laser Science, 2005, vol. 1, pp. 365–367.
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2005 | Journal Article | IST-REx-ID: 6153
M. de Bono and A. Villu Maricq, “Neuronal substrates of complex behaviors in C. elegans,” Annual Review of Neuroscience, vol. 28. Annual Reviews, pp. 451–501, 2005.
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2005 | Journal Article | IST-REx-ID: 6154
B. H. H. Cheung, M. Cohen, C. Rogers, O. Albayram, and M. de Bono, “Experience-dependent modulation of C. elegans behavior by ambient oxygen,” Current Biology, vol. 15, no. 10. Elsevier, pp. 905–917, 2005.
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2005 | Journal Article | IST-REx-ID: 8028 | OA
T. P. Vogels and L. F. Abbott, “Signal propagation and logic gating in networks of integrate-and-fire neurons,” Journal of Neuroscience, vol. 25, no. 46. Society for Neuroscience, pp. 10786–10795, 2005.
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2005 | Journal Article | IST-REx-ID: 8029
T. P. Vogels, K. Rajan, and L. F. Abbott, “Neural network dynamics,” Annual Review of Neuroscience, vol. 28, no. 1. Annual Reviews, pp. 357–376, 2005.
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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.
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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: 843
L. Yampolsky, F. Kondrashov, and A. Kondrashov, “Distribution of the strength of selection against amino acid replacements in human proteins,” Human Molecular Genetics, vol. 14, no. 21. Oxford University Press, pp. 3191–3201, 2005.
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2005 | Journal Article | IST-REx-ID: 8491
P. Schanda, Ē. Kupče, and B. Brutscher, “SOFAST-HMQC experiments for recording two-dimensional deteronuclear correlation spectra of proteins within a few seconds,” Journal of Biomolecular NMR, vol. 33, no. 4. Springer Nature, pp. 199–211, 2005.
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2005 | Journal Article | IST-REx-ID: 8492
P. Schanda and B. Brutscher, “Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds,” Journal of the American Chemical Society, vol. 127, no. 22. American Chemical Society, pp. 8014–8015, 2005.
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2005 | Journal Article | IST-REx-ID: 8516
J. Bourgain and V. Kaloshin, “On diffusion in high-dimensional Hamiltonian systems,” Journal of Functional Analysis, vol. 229, no. 1. Elsevier, pp. 1–61, 2005.
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2005 | Journal Article | IST-REx-ID: 877
F. Kondrashov, “The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution,” Biofizika, vol. 50, no. 3. Pleiades Publishing, pp. 389–395, 2005.
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2005 | Journal Article | IST-REx-ID: 878
F. Kondrashov, “In search of the limits of evolution,” Nature Genetics, vol. 37, no. 1. Nature Publishing Group, pp. 9–10, 2005.
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2005 | Journal Article | IST-REx-ID: 882
F. Kondrashov, “Prediction of pathogenic mutations in mitochondrially encoded human tRNAs,” Human Molecular Genetics, vol. 14, no. 16. Oxford University Press, pp. 2415–2419, 2005.
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2005 | Journal Article | IST-REx-ID: 880
F. Kondrashov, “The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus,” Biofizika, vol. 50, no. 3. Pleiades Publishing, pp. 396–403, 2005.
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2005 | Journal Article | IST-REx-ID: 893
I. Jordan et al., “A universal trend of amino acid gain and loss in protein evolution,” Nature, vol. 433, no. 7026. Nature Publishing Group, pp. 633–638, 2005.
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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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2005 | Journal Article | IST-REx-ID: 13431
S. K. Smoukov, K. J. M. Bishop, R. Klajn, C. J. Campbell, and B. A. Grzybowski, “Cutting into solids with micropatterned gels,” Advanced Materials, vol. 17, no. 11. Wiley, pp. 1361–1365, 2005.
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2005 | Journal Article | IST-REx-ID: 13433
D. Witt, R. Klajn, P. Barski, and B. Grzybowski, “Applications, properties and synthesis of w-functionalized n-alkanethiols and disulfides - the building blocks of self-assembled monolayers,” Current Organic Chemistry, vol. 8, no. 18. Bentham Science, pp. 1763–1797, 2005.
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2005 | Journal Article | IST-REx-ID: 13432
C. J. Campbell, R. Klajn, M. Fialkowski, and B. A. Grzybowski, “One-step multilevel microfabrication by reaction−diffusion,” Langmuir, vol. 21, no. 1. American Chemical Society, pp. 418–423, 2005.
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