Tkadik G, Gregor T. The many bits of positional information. Development. 2021;148(2). doi:10.1242/dev.176065
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Mlynarski WF, Hermundstad AM. Efficient and adaptive sensory codes. Nature Neuroscience. 2021;24:998-1009. doi:10.1038/s41593-021-00846-0
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Zisis T, Schwarz J, Balles M, et al. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 2021;13(30):35545–35560. doi:10.1021/acsami.1c09850
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Gabrielaitis M. Fast and accurate amplitude demodulation of wideband signals. IEEE Transactions on Signal Processing. 2021;69:4039-4054. doi:10.1109/TSP.2021.3087899
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Chalk MJ, Tkadik G, Marre O. Inferring the function performed by a recurrent neural network. PLoS ONE. 2021;16(4). doi:10.1371/journal.pone.0248940
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Kavcic B, Tkadik G, Bollenbach MT. Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. 2021;17. doi:10.1371/journal.pcbi.1008529
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Nagy-Staron AA, Tomasek K, Caruso Carter C, et al. Local genetic context shapes the function of a gene regulatory network. eLife. 2021;10. doi:10.7554/elife.65993
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Mlynarski WF, Hledik M, Sokolowski TR, Tkadik G. Statistical analysis and optimality of neural systems. Neuron. 2021;109(7):1227-1241.e5. doi:10.1016/j.neuron.2021.01.020
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Nardin M, Csicsvari JL, Tkadik G, Savin C. The structure of hippocampal C interactions optimizes spatial coding across experience. bioRxiv. doi:10.1101/2021.09.28.460602
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Lombardi F, Wang JWJL, Zhang X, Ivanov PC. Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality. EPJ Web of Conferences. 2020;230. doi:10.1051/epjconf/202023000005
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Narasimhan M, Johnson AJ, Prizak R, et al. Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. eLife. 2020;9. doi:10.7554/eLife.52067
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Grah R, Friedlander T. Distribution of crosstalk values. 2020. doi:10.1371/journal.pcbi.1007642.s003
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Grah R, Friedlander T. Supporting information. 2020. doi:10.1371/journal.pcbi.1007642.s001
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Berry MJ, Tkadik G. Clustering of neural activity: A design principle for population codes. Frontiers in Computational Neuroscience. 2020;14. doi:10.3389/fncom.2020.00020
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Maoz O, Tkadik G, Esteki MS, Kiani R, Schneidman E. Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(40):25066-25073. doi:10.1073/pnas.1912804117
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Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. Network physiology of cortico–muscular interactions. Frontiers in Physiology. 2020;11. doi:10.3389/fphys.2020.558070
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Grah R, Zoller B, Tkadik G. Nonequilibrium models of optimal enhancer function. PNAS. 2020;117(50):31614-31622. doi:10.1073/pnas.2006731117
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Lombardi F, Gómez-Extremera M, Bernaola-Galván P, et al. 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. Journal of Neuroscience. 2020;40(1):171-190. doi:10.1523/jneurosci.1278-19.2019
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Grah R. Gene regulation across scales – how biophysical constraints shape evolution. 2020. doi:10.15479/AT:ISTA:8155
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Grah R, Zoller B, Tkadik G. Normative models of enhancer function. bioRxiv. 2020. doi:10.1101/2020.04.08.029405
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Grah R, Friedlander T. The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. 2020;16(2). doi:10.1371/journal.pcbi.1007642
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Grah R, Friedlander T. Maximizing crosstalk. 2020. doi:10.1371/journal.pcbi.1007642.s002
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Kavcic B. Analysis scripts and research data for the paper “Mechanisms of drug interactions between translation-inhibiting antibiotics.”10.15479/AT:ISTA:8097__2020. doi:10.15479/AT:ISTA:8097
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Kavcic B. Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.”10.15479/AT:ISTA:8930__2020. doi:10.15479/AT:ISTA:8930
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Grah R. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. 2020. doi:10.15479/AT:ISTA:7383
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Kavcic B. Perturbations of protein synthesis: from antibiotics to genetics and physiology. 2020. doi:10.15479/AT:ISTA:8657
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Kavcic B, Tkadik G, Bollenbach MT. Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. 2020;11. doi:10.1038/s41467-020-17734-z
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Kavcic B, Tkadik G, Bollenbach MT. A minimal biophysical model of combined antibiotic action. bioRxiv. 2020. doi:10.1101/2020.04.18.047886
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Tomanek I, Grah R, Lagator M, et al. Gene amplification as a form of population-level gene expression regulation. Nature Ecology &; Evolution. 2020;4(4):612-625. doi:10.1038/s41559-020-1132-7
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Bialek W, Gregor T, Tkadik G. Action at a distance in transcriptional regulation. arXiv:191208579.
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arXiv: 1912.08579

Petkova MD, Tkadik G, Bialek W, Wieschaus EF, Gregor T. Optimal decoding of cellular identities in a genetic network. Cell. 2019;176(4):844-855.e15. doi:10.1016/j.cell.2019.01.007
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De Martino D. Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical. 2019;52(4). doi:10.1088/1751-8121/aaf2dd
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Mitosch K, Rieckh G, Bollenbach MT. Temporal order and precision of complex stress responses in individual bacteria. Molecular systems biology. 2019;15(2). doi:10.15252/msb.20188470
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Ruess J, Pleska M, Guet CC, Tkadik G. Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. 2019;15(7). doi:10.1371/journal.pcbi.1007168
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Ruess J, Pleska M, Guet CC, Tkadik G. Supporting text and results. 2019. doi:10.1371/journal.pcbi.1007168.s001
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Sokolowski TR, Paijmans J, Bossen L, et al. eGFRD in all dimensions. The Journal of Chemical Physics. 2019;150(5). doi:10.1063/1.5064867
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Cepeda Humerez SA, Ruess J, Tkadik G. Estimating information in time-varying signals. PLoS computational biology. 2019;15(9):e1007290. doi:10.1371/journal.pcbi.1007290
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Lang M, Shkolnikov M. Harmonic dynamics of the Abelian sandpile. Proceedings of the National Academy of Sciences. 2019;116(8):2821-2830. doi:10.1073/pnas.1812015116
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Kavcic B, Sakashita A, Noguchi H, Ziherl P. Limiting shapes of confined lipid vesicles. Soft Matter. 2019;15(4):602-614. doi:10.1039/c8sm01956h
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Cepeda Humerez SA. Estimating information flow in single cells. 2019. doi:10.15479/AT:ISTA:6473
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Prizak R. Coevolution of transcription factors and their binding sites in sequence space. 2019. doi:10.15479/at:ista:th6071
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Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. Non-equilibrium critical dynamics of bursts in ;8 and ;4 rhythms as fundamental characteristic of sleep and wake micro-architecture. PLoS Computational Biology. 2019;15(11). doi:10.1371/journal.pcbi.1007268
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Carballo-Pacheco M, Desponds J, Gavrilchenko T, et al. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 2019;99(2). doi:10.1103/PhysRevE.99.022423
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Hledik M, Sokolowski TR, Tkadik G. A tight upper bound on mutual information. In: IEEE Information Theory Workshop, ITW 2019. IEEE; 2019. doi:10.1109/ITW44776.2019.8989292
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De Martino A, De Martino D. An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. 2018;4(4). doi:10.1016/j.heliyon.2018.e00596
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Misun P, Birchler A, Lang M, Hierlemann A, Frey O. Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. 2018;1771:183-202. doi:10.1007/978-1-4939-7792-5_15
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Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkadik G, Swain P. Distributed and dynamic intracellular organization of extracellular information. PNAS. 2018;115(23):6088-6093. doi:10.1073/pnas.1716659115
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Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 2018;209(3):861-883. doi:10.1534/genetics.118.300748
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Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Supplemental material for Bodova et al., 2018. 2018. doi:10.25386/genetics.6148304.v1
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Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkadik G. Probabilistic models of individual and collective animal behavior. PLoS One. 2018;13(3). doi:10.1371/journal.pone.0193049
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Pleska M, Lang M, Refardt D, Levin B, Guet CC. Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. 2018;2(2):359-366. doi:10.1038/s41559-017-0424-z
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Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkadik G. Implementation of the inference method in Matlab. 2018. doi:10.1371/journal.pone.0193049.s001
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Ferrari U, Deny S, Chalk MJ, Tkadik G, Marre O, Mora T. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 2018;98(4). doi:10.1103/PhysRevE.98.042410
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Chalk MJ, Marre O, Tkadik G. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 2018;115(1):186-191. doi:10.1073/pnas.1711114115
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Bodova K, Haskovec J, Markowich P. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 2018;376-377:108-120. doi:10.1016/j.physd.2017.10.015
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Palmer A, Chait RP, Kishony R. Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. 2018;35(11):2669-2684. doi:10.1093/molbev/msy163
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Botella Soler V, Deny S, Martius GS, Marre O, Tkadik G. Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology. 2018;14(5). doi:10.1371/journal.pcbi.1006057
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Deny S, Marre O, Botella-Soler V, Martius GS, Tkadik G. Nonlinear decoding of a complex movie from the mammalian retina. 2018. doi:10.15479/AT:ISTA:98
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De Martino D, Mc AA, Bergmiller T, Guet CC, Tkadik G. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-05417-9
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De Martino D, Tkadik G. Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.”10.15479/AT:ISTA:62__2018. doi:10.15479/AT:ISTA:62
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Igler C, Lagator M, Tkadik G, Bollback JP, Guet CC. Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. 2018;2(10):1633-1643. doi:10.1038/s41559-018-0651-y
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Igler C, Lagator M, Tkadik G, Bollback JP, Guet CC. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. 2018. doi:10.15479/AT:ISTA:108
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Chait RP, Ruess J, Bergmiller T, Tkadik G, Guet CC. Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-01683-1
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Der R, Martius GS. Dynamical self consistency leads to behavioral development and emergent social interactions in robots. In: IEEE; 2017. doi:10.1109/DEVLRN.2016.7846789
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Der R, Martius GS. Self organized behavior generation for musculoskeletal robots. Frontiers in Neurorobotics. 2017;11(MAR). doi:10.3389/fnbot.2017.00008
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Humplik J, Tkadik G. Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. 2017;13(9). doi:10.1371/journal.pcbi.1005763
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Harpaz R, Tkadik G, Schneidman E. Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. 2017;114(38):10149-10154. doi:10.1073/pnas.1703817114
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Prentice J, Marre O, Ioffe M, Loback A, Tkadik G, Berry M. Data from: Error-robust modes of the retinal population code. 2017. doi:10.5061/dryad.1f1rc
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Chalk MJ, Masset P, Gutkin B, Denève S. Sensory noise predicts divisive reshaping of receptive fields. PLoS Computational Biology. 2017;13(6). doi:10.1371/journal.pcbi.1005582
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Chalk MJ, Masset P, Gutkin B, Denève S. Supplementary appendix. 2017. doi:10.1371/journal.pcbi.1005582.s001
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Mitosch K, Rieckh G, Bollenbach MT. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. 2017;4(4):393-403. doi:10.1016/j.cels.2017.03.001
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Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of Statistics. 2017;44(2):285-306. doi:10.1111/sjos.12251
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Deny S, Ferrari U, Mace E, et al. Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-02159-y
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Levina (Martius) A, Priesemann V. Subsampling scaling. Nature Communications. 2017;8. doi:10.1038/ncomms15140
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Friedlander T, Prizak R, Barton NH, Tkadik G. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-00238-8
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De Martino D. Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. 10.1103/PhysRevE.95.062419__Physical Review E Statistical Nonlinear and Soft Matter Physics . 2017;95(6):062419. doi:10.1103/PhysRevE.95.062419
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De Martino D, Capuani F, De Martino A. Quantifying the entropic cost of cellular growth control. 10.1103/PhysRevE.96.010401__Physical Review E Statistical Nonlinear and Soft Matter Physics . 2017;96(1). doi:10.1103/PhysRevE.96.010401
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Zagórski MP, Tabata Y, Brandenberg N, et al. Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. 2017;356(6345):1379-1383. doi:10.1126/science.aam5887
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Colabrese S, De Martino D, Leuzzi L, Marinari E. Phase transitions in integer linear problems. 10.1088/1742-5468/aa85c3__Journal of Statistical Mechanics: Theory and Experiment. 2017;2017(9). doi:10.1088/1742-5468/aa85c3
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Savin C, Tkadik G. Maximum entropy models as a tool for building precise neural controls. Current Opinion in Neurobiology. 2017;46:120-126. doi:10.1016/j.conb.2017.08.001
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De Martino D. Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. Physical Review E. 2017;96(6). doi:10.1103/PhysRevE.96.060401
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Lang M, Sontag E. Zeros of nonlinear systems with input invariances. Automatica. 2017;81C:46-55. doi:10.1016/j.automatica.2017.03.030
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Marre O, Tkadik G, Amodei D, Schneidman E, Bialek W, Berry M. Multi-electrode array recording from salamander retinal ganglion cells. 2017. doi:10.15479/AT:ISTA:61
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Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. 2017. doi:10.15479/AT:ISTA:53
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Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science. 2017;356(6335):311-315. doi:10.1126/science.aaf4762
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Chalk MJ, Marre O, Tkadik G. Relevant sparse codes with variational information bottleneck. In: Vol 29. Neural Information Processing Systems; 2016:1965-1973.
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Savin C, Tkadik G. Estimating nonlinear neural response functions using GP priors and Kronecker methods. In: Vol 29. Neural Information Processing Systems; 2016:3610-3618.
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Lang M, Stelling J. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 2016;38(6):8-08. doi:10.1137/15M103306X
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Tkadik G. Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on &;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&;quot; by O. C. Martin et al. Physics of Life Reviews. 2016;17:166-167. doi:10.1016/j.plrev.2016.06.005
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De Martino D, Masoero D. Asymptotic analysis of noisy fitness maximization, applied to metabolism &;amp; growth. 10.1088/1742-5468/aa4e8f__Journal of Statistical Mechanics: Theory and Experiment. 2016;2016(12). doi:10.1088/1742-5468/aa4e8f
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Hu F, Rishishwar L, Sivadas A, et al. Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. Journal of Clinical Microbiology. 2016;54(12):3010-3017. doi:10.1128/JCM.01511-16
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Martius GS, Hostettler R, Knoll A, Der R. Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm. In: Vol 2016-November. IEEE; 2016. doi:10.1109/IROS.2016.7759138
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Miki G, Stoll A, Bevirt J, Grah R, Moore M. Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency. In: AIAA; 2016:1-19. doi:10.2514/6.2016-3764
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Sokolowski TR, Walczak A, Bialek W, Tkadik G. Extending the dynamic range of transcription factor action by translational regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2016;93(2). doi:10.1103/PhysRevE.93.022404
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Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. PNAS. 2016;113(7):1811-1816. doi:10.1073/pnas.1419248113
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Tkadik G, Bialek W. Information processing in living systems. Annual Review of Condensed Matter Physics. 2016;7:89-117. doi:10.1146/annurev-conmatphys-031214-014803
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De Martino D. The dual of the space of interactions in neural network models. International Journal of Modern Physics C. 2016;27(6). doi:10.1142/S0129183116500674
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Chalk MJ, Gutkin B, Denève S. Neural oscillations as a signature of efficient coding in the presence of synaptic delays. eLife. 2016;5(2016JULY). doi:10.7554/eLife.13824
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Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. 2016;12(11):902-904. doi:10.1038/nchembio.2176
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