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112 Publications

2019 | Journal Article | IST-REx-ID: 6046   OA
Mitosch, K., Rieckh, G., & Bollenbach, M. T. (2019). Temporal order and precision of complex stress responses in individual bacteria. Molecular Systems Biology, 15(2), e8470. https://doi.org/10.15252/msb.20188470
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2019 | Journal Article | IST-REx-ID: 5817
Kavcic, B., Sakashita, A., Noguchi, H., & Ziherl, P. (2019). Limiting shapes of confined lipid vesicles. Soft Matter, 15(4), 602–614. https://doi.org/10.1039/c8sm01956h
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2019 | Thesis | IST-REx-ID: 6473
Cepeda Humerez, S. A. (2019). Estimating information flow in single cells. IST Austria. https://doi.org/10.15479/AT:ISTA:6473
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2019 | Journal Article | IST-REx-ID: 5945
Petkova, M. D., Tkacik, G., Bialek, W., Wieschaus, E. F., & Gregor, T. (2019). Optimal decoding of cellular identities in a genetic network. Cell, 176(4), 844–855.e15. https://doi.org/10.1016/j.cell.2019.01.007
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2019 | Journal Article | IST-REx-ID: 6049   OA
De Martino, D. (2019). Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical, 52(4), 045002. https://doi.org/10.1088/1751-8121/aaf2dd
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2019 | Journal Article | IST-REx-ID: 6784   OA
Ruess, J., Pleska, M., Guet, C. C., & Tkačik, G. (2019). Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology, 15(7). https://doi.org/10.1371/journal.pcbi.1007168
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2019 | Journal Article | IST-REx-ID: 6090   OA
Carballo-Pacheco, M., Desponds, J., Gavrilchenko, T., Mayer, A., Prizak, R., Reddy, G., … Mora, T. (2019). Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E, 99(2), 022423. https://doi.org/10.1103/PhysRevE.99.022423
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2019 | Thesis | IST-REx-ID: 6071   OA
Prizak, R. (2019). Coevolution of transcription factors and their binding sites in sequence space. IST Austria. https://doi.org/10.15479/at:ista:th6071
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2018 | Journal Article | IST-REx-ID: 31   OA
Ferrari, U., Deny, S., Chalk, M. J., Tkacik, G., Marre, O., & Mora, T. (2018). Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E, 98(4). https://doi.org/10.1103/PhysRevE.98.042410
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2018 | Journal Article | IST-REx-ID: 543   OA
Chalk, M. J., Marre, O., & Tkacik, G. (2018). Toward a unified theory of efficient, predictive, and sparse coding. PNAS, 115(1), 186–191. https://doi.org/10.1073/pnas.1711114115
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2018 | Research Data | IST-REx-ID: 5587   OA
De Martino, D., & Tkacik, G. (2018). Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” IST Austria. https://doi.org/10.15479/AT:ISTA:62
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2018 | Journal Article | IST-REx-ID: 67
Igler, C., Lagator, M., Tkacik, G., Bollback, J. P., & Guet, C. C. (2018). Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution, 2(10), 1633–1643. https://doi.org/10.1038/s41559-018-0651-y
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2018 | Journal Article | IST-REx-ID: 316   OA
Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018). Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics, 209(3), 861–883. https://doi.org/10.1534/genetics.118.300748
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2018 | Journal Article | IST-REx-ID: 607   OA
Bodova, K., Haskovec, J., & Markowich, P. (2018). Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena, 376377, 108–120. https://doi.org/10.1016/j.physd.2017.10.015
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2018 | Journal Article | IST-REx-ID: 19   OA
Palmer, A., Chait, R. P., & Kishony, R. (2018). Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution, 35(11), 2669–2684. https://doi.org/10.1093/molbev/msy163
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2018 | Preprint | IST-REx-ID: 196   OA
Lang, M., & Shkolnikov, M. (2018). Harmonic dynamics of the Abelian sandpile. ArXiv. ArXiv.
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2018 | Journal Article | IST-REx-ID: 305
Misun, P., Birchler, A., Lang, M., Hierlemann, A., & Frey, O. (2018). Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology, 1771, 183–202. https://doi.org/10.1007/978-1-4939-7792-5_15
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2018 | Journal Article | IST-REx-ID: 406   OA
Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkacik, G. (2018). Probabilistic models of individual and collective animal behavior. PLoS One, 13(3). https://doi.org/10.1371/journal.pone.0193049
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2018 | Journal Article | IST-REx-ID: 292
Botella Soler, V., Deny, S., Martius, G. S., Marre, O., & Tkacik, G. (2018). Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology, 14(5), e1006057. https://doi.org/10.1371/journal.pcbi.1006057
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2018 | Research Data | IST-REx-ID: 5584   OA
Deny, S., Marre, O., Botella-Soler, V., Martius, G. S., & Tkacik, G. (2018). Nonlinear decoding of a complex movie from the mammalian retina. IST Austria. https://doi.org/10.15479/AT:ISTA:98
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2018 | Journal Article | IST-REx-ID: 306   OA
De Martino, A., & De Martino, D. (2018). An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon, 4(4). https://doi.org/10.1016/j.heliyon.2018.e00596
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2018 | Journal Article | IST-REx-ID: 161
De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., & Tkacik, G. (2018). Statistical mechanics for metabolic networks during steady state growth. Nature Communications, 9(1), 2988. https://doi.org/10.1038/s41467-018-05417-9
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2018 | Journal Article | IST-REx-ID: 281
Granados, A., Pietsch, J., Cepeda Humerez, S. A., Farquhar, I., Tkacik, G., & Swain, P. (2018). Distributed and dynamic intracellular organization of extracellular information. PNAS, 115(23), 6088–6093. https://doi.org/10.1073/pnas.1716659115
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2018 | Research Data | IST-REx-ID: 5585
Igler, C., Lagator, M., Tkacik, G., Bollback, J. P., & Guet, C. C. (2018). Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. IST Austria. https://doi.org/10.15479/AT:ISTA:108
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2018 | Journal Article | IST-REx-ID: 457
Pleska, M., Lang, M., Refardt, D., Levin, B., & Guet, C. C. (2018). Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution, 2(2), 359–366. https://doi.org/10.1038/s41559-017-0424-z
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2017 | Journal Article | IST-REx-ID: 1104   OA
Deny, S., Ferrari, U., Mace, E., Yger, P., Caplette, R., Picaud, S., … Marre, O. (2017). Multiplexed computations in retinal ganglion cells of a single type. Nature Communications, 8(1). https://doi.org/10.1038/s41467-017-02159-y
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2017 | Research Data | IST-REx-ID: 5562   OA
Marre, O., Tkacik, G., Amodei, D., Schneidman, E., Bialek, W., & Berry, M. (2017). Multi-electrode array recording from salamander retinal ganglion cells. IST Austria. https://doi.org/10.15479/AT:ISTA:61
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2017 | Journal Article | IST-REx-ID: 720   OA
Humplik, J., & Tkacik, G. (2017). Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology, 13(9). https://doi.org/10.1371/journal.pcbi.1005763
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2017 | Journal Article | IST-REx-ID: 725   OA
Harpaz, R., Tkacik, G., & Schneidman, E. (2017). Discrete modes of social information processing predict individual behavior of fish in a group. PNAS, 114(38), 10149–10154. https://doi.org/10.1073/pnas.1703817114
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2017 | Journal Article | IST-REx-ID: 548   OA
De Martino, D. (2017). Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. Physical Review E, 96(6). https://doi.org/10.1103/PhysRevE.96.060401
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2017 | Journal Article | IST-REx-ID: 613   OA
Chait, R. P., Ruess, J., Bergmiller, T., Tkacik, G., & Guet, C. C. (2017). Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications, 8(1). https://doi.org/10.1038/s41467-017-01683-1
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2017 | Journal Article | IST-REx-ID: 947   OA
De Martino, D., Capuani, F., & De Martino, A. (2017). Quantifying the entropic cost of cellular growth control. Physical Review E Statistical Nonlinear and Soft Matter Physics , 96(1). https://doi.org/10.1103/PhysRevE.96.010401
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2017 | Journal Article | IST-REx-ID: 959   OA
De Martino, D. (2017). Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. Physical Review E Statistical Nonlinear and Soft Matter Physics , 95(6), 062419. https://doi.org/10.1103/PhysRevE.95.062419
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2017 | Conference Paper | IST-REx-ID: 652
Der, R., & Martius, G. S. (2017). Dynamical self consistency leads to behavioral development and emergent social interactions in robots. Presented at the ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics , Cergy-Pontoise, France: IEEE. https://doi.org/10.1109/DEVLRN.2016.7846789
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2017 | Journal Article | IST-REx-ID: 823   OA
Colabrese, S., De Martino, D., Leuzzi, L., & Marinari, E. (2017). Phase transitions in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment, 2017(9). https://doi.org/10.1088/1742-5468/aa85c3
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2017 | Journal Article | IST-REx-ID: 943   OA
Zagórski, M. P., Tabata, Y., Brandenberg, N., Lutolf, M., Tkacik, G., Bollenbach, T., … Kicheva, A. (2017). Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science, 356(6345), 1379–1383. https://doi.org/10.1126/science.aam5887
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2017 | Journal Article | IST-REx-ID: 993   OA
Levina (Martius), A., & Priesemann, V. (2017). Subsampling scaling. Nature Communications, 8. https://doi.org/10.1038/ncomms15140
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2017 | Journal Article | IST-REx-ID: 955
Friedlander, T., Prizak, R., Barton, N. H., & Tkacik, G. (2017). Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications, 8(1). https://doi.org/10.1038/s41467-017-00238-8
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2017 | Journal Article | IST-REx-ID: 658   OA
Der, R., & Martius, G. S. (2017). Self organized behavior generation for musculoskeletal robots. Frontiers in Neurorobotics, 11(MAR). https://doi.org/10.3389/fnbot.2017.00008
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2017 | Journal Article | IST-REx-ID: 665
Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild, R., … Guet, C. C. (2017). Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science, 356(6335), 311–315. https://doi.org/10.1126/science.aaf4762
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2017 | Research Data | IST-REx-ID: 5560
Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild, R., … Guet, C. C. (2017). Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. IST Austria. https://doi.org/doi:10.15479/AT:ISTA:53
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2017 | Journal Article | IST-REx-ID: 730
Savin, C., & Tkacik, G. (2017). Maximum entropy models as a tool for building precise neural controls. Current Opinion in Neurobiology, 46, 120–126. https://doi.org/10.1016/j.conb.2017.08.001
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2017 | Journal Article | IST-REx-ID: 735
Barone, V., Lang, M., Krens, G., Pradhan, S., Shamipour, S., Sako, K., … Heisenberg, C.-P. J. (2017). An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. Developmental Cell, 43(2), 198–211. https://doi.org/10.1016/j.devcel.2017.09.014
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2017 | Journal Article | IST-REx-ID: 2016   OA
Martin Del Campo Sanchez, A., Cepeda Humerez, S. A., & Uhler, C. (2017). Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of Statistics, 44(2), 285–306. https://doi.org/10.1111/sjos.12251
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2017 | Journal Article | IST-REx-ID: 1007   OA
Lang, M., & Sontag, E. (2017). Zeros of nonlinear systems with input invariances. Automatica, 81C, 46–55. https://doi.org/10.1016/j.automatica.2017.03.030
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2017 | Journal Article | IST-REx-ID: 680   OA
Chalk, M. J., Masset, P., Gutkin, B., & Denève, S. (2017). Sensory noise predicts divisive reshaping of receptive fields. PLoS Computational Biology, 13(6). https://doi.org/10.1371/journal.pcbi.1005582
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2017 | Journal Article | IST-REx-ID: 666   OA
Mitosch, K., Rieckh, G., & Bollenbach, T. (2017). Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems, 4(4), 393–403. https://doi.org/10.1016/j.cels.2017.03.001
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2016 | Journal Article | IST-REx-ID: 1197   OA
Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkacik, G., & Berry, M. (2016). Error-robust modes of the retinal population code. PLoS Computational Biology, 12(11). https://doi.org/10.1371/journal.pcbi.1005148
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2016 | Journal Article | IST-REx-ID: 1248   OA
Tkacik, G., & Bialek, W. (2016). Information processing in living systems. Annual Review of Condensed Matter Physics, 7, 89–117. https://doi.org/10.1146/annurev-conmatphys-031214-014803
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2016 | Conference Paper | IST-REx-ID: 1320
Lang, M., & Sontag, E. (2016). Scale-invariant systems realize nonlinear differential operators (Vol. 2016–July). Presented at the ACC: American Control Conference, Boston, MA, USA: IEEE. https://doi.org/10.1109/ACC.2016.7526722
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