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124 Publications

2020 | Preprint | IST-REx-ID: 7463   OA
Lombardi F, Shriki O, Herrmann HJ, de Arcangelis L. 2020. Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. bioRxiv.
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2020 | Journal Article | IST-REx-ID: 7569   OA
Grah R, Friedlander T. 2020. The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. 16(2), e1007642.
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2020 | Journal Article | IST-REx-ID: 7490   OA
Narasimhan M, Johnson AJ, Prizak R, Kaufmann W, Tan S, Casillas Perez BE, Friml J. 2020. Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. eLife. 9, e52067.
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2020 | Preprint | IST-REx-ID: 7553   OA
Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. Statistical analysis and optimality of biological systems. bioRxiv.
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2020 | Journal Article | IST-REx-ID: 7251
Lombardi F, Gómez-Extremera M, Bernaola-Galván P, Vetrivelan R, Saper CB, Scammell TE, Ivanov PC. 2020. Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake. The Journal of neuroscience. 40(1), 171–190.
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2020 | Research Data | IST-REx-ID: 7383   OA
Grah R. 2020. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation, IST Austria,p.
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2019 | Journal Article | IST-REx-ID: 6046   OA
Mitosch K, Rieckh G, Bollenbach MT. 2019. Temporal order and precision of complex stress responses in individual bacteria. Molecular systems biology. 15(2), e8470.
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2019 | Journal Article | IST-REx-ID: 7103   OA
Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. 2019. Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. PLOS Computational Biology. 15(11), e1007268.
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2019 | Preprint | IST-REx-ID: 7083   OA
Kavcic B, Tkačik G, Bollenbach T. Mechanistic origin of drug interactions between translation-inhibiting antibiotics. bioRxiv.
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2019 | Preprint | IST-REx-ID: 7552   OA
Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. arXiv:1912.08579.
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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.
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2019 | Thesis | IST-REx-ID: 6473
Cepeda Humerez SA. 2019. Estimating information flow in single cells, IST Austria, 135p.
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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.
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2019 | Journal Article | IST-REx-ID: 6784   OA
Ruess J, Pleska M, Guet CC, Tkačik G. 2019. Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. 15(7), e1007168.
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2019 | Journal Article | IST-REx-ID: 5945
Petkova MD, Tkacik G, Bialek W, Wieschaus EF, Gregor T. 2019. Optimal decoding of cellular identities in a genetic network. Cell. 176(4), 844–855.e15.
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2019 | Journal Article | IST-REx-ID: 7422   OA
Sokolowski TR, Paijmans J, Bossen L, Miedema T, Wehrens M, Becker NB, Kaizu K, Takahashi K, Dogterom M, ten Wolde PR. 2019. eGFRD in all dimensions. The Journal of Chemical Physics. 150(5), 054108.
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2019 | Journal Article | IST-REx-ID: 6900   OA
Cepeda Humerez SA, Ruess J, Tkačik G. 2019. Estimating information in time-varying signals. PLoS computational biology. 15(9), e1007290.
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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, Nemenman I, Mora T. 2019. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 99(2), 022423.
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2019 | Thesis | IST-REx-ID: 6071
Prizak R. 2019. Coevolution of transcription factors and their binding sites in sequence space, IST Austria, 189p.
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2019 | Conference Paper | IST-REx-ID: 7606   OA
Hledik M, Sokolowski TR, Tkačik G. 2019. A tight upper bound on mutual information. IEEE Information Theory Workshop, ITW 2019. Information Theory Workshop 8989292.
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2018 | Journal Article | IST-REx-ID: 31   OA
Ferrari U, Deny S, Chalk MJ, Tkacik G, Marre O, Mora T. 2018. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 98(4), 042410.
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2018 | Journal Article | IST-REx-ID: 543   OA
Chalk MJ, Marre O, Tkacik G. 2018. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 115(1), 186–191.
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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,p.
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2018 | Journal Article | IST-REx-ID: 67
Igler C, Lagator M, Tkacik G, Bollback JP, Guet CC. 2018. Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. 2(10), 1633–1643.
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2018 | Journal Article | IST-REx-ID: 316   OA
Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 209(3), 861–883.
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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. 376–377, 108–120.
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2018 | Journal Article | IST-REx-ID: 19   OA
Palmer A, Chait RP, Kishony R. 2018. Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. 35(11), 2669–2684.
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2018 | Preprint | IST-REx-ID: 196   OA
Lang M, Shkolnikov M. 2018. Harmonic dynamics of the Abelian sandpile. 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.
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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).
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2018 | Journal Article | IST-REx-ID: 292   OA
Botella Soler V, Deny S, Martius GS, Marre O, Tkacik G. 2018. Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology. 14(5), e1006057.
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2018 | Research Data | IST-REx-ID: 5584
Deny S, Marre O, Botella-Soler V, Martius GS, Tkacik G. 2018. Nonlinear decoding of a complex movie from the mammalian retina, IST Austria,p.
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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), e00596.
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2018 | Journal Article | IST-REx-ID: 457
Pleska M, Lang M, Refardt D, Levin B, Guet CC. 2018. Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. 2(2), 359–366.
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2018 | Journal Article | IST-REx-ID: 281   OA
Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkacik G, Swain P. 2018. Distributed and dynamic intracellular organization of extracellular information. PNAS. 115(23), 6088–6093.
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2018 | Journal Article | IST-REx-ID: 161
De Martino D, Mc AA, Bergmiller T, Guet CC, Tkacik G. 2018. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 9(1), 2988.
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2018 | Research Data | IST-REx-ID: 5585   OA
Igler C, Lagator M, Tkacik G, Bollback JP, Guet CC. 2018. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring, IST Austria,p.
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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,p.
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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.
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2017 | Journal Article | IST-REx-ID: 1104   OA
Deny S, Ferrari U, Mace E, Yger P, Caplette R, Picaud S, Tkacik G, Marre O. 2017. Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. 8(1), 1964.
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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), e1005763.
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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), 060401.
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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), 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.
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2017 | Journal Article | IST-REx-ID: 613   OA
Chait RP, Ruess J, Bergmiller T, Tkacik G, Guet CC. 2017. Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. 8(1), 1535.
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2017 | Conference Paper | IST-REx-ID: 652
Der R, Martius GS. 2017. Dynamical self consistency leads to behavioral development and emergent social interactions in robots. ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics
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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), 093404.
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2017 | Journal Article | IST-REx-ID: 993   OA
Levina (Martius) A, Priesemann V. 2017. Subsampling scaling. Nature Communications. 8, 15140.
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2017 | Journal Article | IST-REx-ID: 943   OA
Zagórski MP, Tabata Y, Brandenberg N, Lutolf M, Tkacik G, Bollenbach T, Briscoe J, Kicheva A. 2017. Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. 356(6345), 1379–1383.
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2017 | Journal Article | IST-REx-ID: 955   OA
Friedlander T, Prizak R, Barton NH, Tkacik G. 2017. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 8(1), 216.
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