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113 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: 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 | 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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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 | 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: 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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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 | 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
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 | 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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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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2017 | Journal Article | IST-REx-ID: 658   OA
Der R, Martius GS. 2017. Self organized behavior generation for musculoskeletal robots. Frontiers in Neurorobotics. 11(MAR), 00008.
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2017 | Journal Article | IST-REx-ID: 2016
Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. 2017. Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of Statistics. 44(2), 285–306.
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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.
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2017 | Journal Article | IST-REx-ID: 735
Barone V, Lang M, Krens G, Pradhan S, Shamipour S, Sako K, Sikora MK, Guet CC, Heisenberg C-PJ. 2017. An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. Developmental Cell. 43(2), 198–211.
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2017 | Journal Article | IST-REx-ID: 665
Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkacik G, Guet CC. 2017. Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science. 356(6335), 311–315.
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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.
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2017 | Journal Article | IST-REx-ID: 680   OA
Chalk MJ, Masset P, Gutkin B, Denève S. 2017. Sensory noise predicts divisive reshaping of receptive fields. PLoS Computational Biology. 13(6), e1005582.
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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.
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2016 | Thesis | IST-REx-ID: 1128
Rieckh G. 2016. Studying the complexities of transcriptional regulation, IST Austria, 114p.
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2016 | Conference Paper | IST-REx-ID: 1320
Lang M, Sontag E. 2016. Scale-invariant systems realize nonlinear differential operators. ACC: American Control Conference vol. 2016–July.
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