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128 Publications

2018 | Journal Article | IST-REx-ID: 457
M. Pleska, M. Lang, D. Refardt, B. Levin, and C. C. Guet, “Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity,” Nature Ecology and Evolution, vol. 2, no. 2, pp. 359–366, 2018.
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2018 | Journal Article | IST-REx-ID: 543 | OA
M. J. Chalk, O. Marre, and G. Tkacik, “Toward a unified theory of efficient, predictive, and sparse coding,” PNAS, vol. 115, no. 1, pp. 186–191, 2018.
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2018 | Journal Article | IST-REx-ID: 607 | OA
K. Bodova, J. Haskovec, and P. Markowich, “Well posedness and maximum entropy approximation for the dynamics of quantitative traits,” Physica D: Nonlinear Phenomena, vol. 376–377, pp. 108–120, 2018.
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2018 | Journal Article | IST-REx-ID: 281 | OA
A. Granados, J. Pietsch, S. A. Cepeda Humerez, I. Farquhar, G. Tkacik, and P. Swain, “Distributed and dynamic intracellular organization of extracellular information,” PNAS, vol. 115, no. 23, pp. 6088–6093, 2018.
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2018 | Journal Article | IST-REx-ID: 292 | OA
V. Botella Soler, S. Deny, G. S. Martius, O. Marre, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina,” PLoS Computational Biology, vol. 14, no. 5, 2018.
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2018 | Journal Article | IST-REx-ID: 305
P. Misun, A. Birchler, M. Lang, A. Hierlemann, and O. Frey, “Fabrication and operation of microfluidic hanging drop networks,” Methods in Molecular Biology, vol. 1771, pp. 183–202, 2018.
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2018 | Journal Article | IST-REx-ID: 306 | OA
A. De Martino and D. De Martino, “An introduction to the maximum entropy approach and its application to inference problems in biology,” Heliyon, vol. 4, no. 4, 2018.
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2018 | Journal Article | IST-REx-ID: 31 | OA
U. Ferrari, S. Deny, M. J. Chalk, G. Tkacik, O. Marre, and T. Mora, “Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons,” Physical Review E, vol. 98, no. 4, p. 042410, 2018.
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2018 | Journal Article | IST-REx-ID: 67 | OA
C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Evolutionary potential of transcription factors for gene regulatory rewiring,” Nature Ecology and Evolution, vol. 2, no. 10, pp. 1633–1643, 2018.
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2018 | Journal Article | IST-REx-ID: 161 | OA
D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical mechanics for metabolic networks during steady state growth,” Nature Communications, vol. 9, no. 1, 2018.
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2018 | Journal Article | IST-REx-ID: 19 | OA
A. Palmer, R. P. Chait, and R. Kishony, “Nonoptimal gene expression creates latent potential for antibiotic resistance,” Molecular Biology and Evolution, vol. 35, no. 11, pp. 2669–2684, 2018.
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2018 | Journal Article | IST-REx-ID: 316 | OA
K. Bod’ová, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system,” Genetics, vol. 209, no. 3, pp. 861–883, 2018.
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2017 | Journal Article | IST-REx-ID: 2016 | OA
A. Martin Del Campo Sanchez, S. A. Cepeda Humerez, and C. Uhler, “Exact goodness-of-fit testing for the Ising model,” Scandinavian Journal of Statistics, vol. 44, no. 2, pp. 285–306, 2017.
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2017 | Journal Article | IST-REx-ID: 720 | OA
J. Humplik and G. Tkačik, “Probabilistic models for neural populations that naturally capture global coupling and criticality,” PLoS Computational Biology, vol. 13, no. 9, 2017.
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2017 | Journal Article | IST-REx-ID: 725 | OA
R. Harpaz, G. Tkacik, and E. Schneidman, “Discrete modes of social information processing predict individual behavior of fish in a group,” PNAS, vol. 114, no. 38, pp. 10149–10154, 2017.
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2017 | Journal Article | IST-REx-ID: 730
C. Savin and G. Tkacik, “Maximum entropy models as a tool for building precise neural controls,” Current Opinion in Neurobiology, vol. 46, pp. 120–126, 2017.
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2017 | Journal Article | IST-REx-ID: 735
V. Barone et al., “An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate,” Developmental Cell, vol. 43, no. 2, pp. 198–211, 2017.
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2017 | Journal Article | IST-REx-ID: 548 | OA
D. De Martino, “Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes,” Physical Review E, vol. 96, no. 6, 2017.
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2017 | Journal Article | IST-REx-ID: 613 | OA
R. P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, and C. C. Guet, “Shaping bacterial population behavior through computer interfaced control of individual cells,” Nature Communications, vol. 8, no. 1, 2017.
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2017 | Conference Paper | IST-REx-ID: 652
R. Der and G. S. Martius, “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, 2017.
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2017 | Journal Article | IST-REx-ID: 658 | OA
R. Der and G. S. Martius, “Self organized behavior generation for musculoskeletal robots,” Frontiers in Neurorobotics, vol. 11, no. MAR, 2017.
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2017 | Journal Article | IST-REx-ID: 665
T. Bergmiller et al., “Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity,” Science, vol. 356, no. 6335, pp. 311–315, 2017.
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2017 | Journal Article | IST-REx-ID: 666 | OA
K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment,” Cell Systems, vol. 4, no. 4, pp. 393–403, 2017.
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2017 | Journal Article | IST-REx-ID: 680 | OA
M. J. Chalk, P. Masset, B. Gutkin, and S. Denève, “Sensory noise predicts divisive reshaping of receptive fields,” PLoS Computational Biology, vol. 13, no. 6, 2017.
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2017 | Journal Article | IST-REx-ID: 823 | OA
S. Colabrese, D. De Martino, L. Leuzzi, and E. Marinari, “Phase transitions in integer linear problems,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2017, no. 9, 2017.
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2017 | Journal Article | IST-REx-ID: 943 | OA
M. P. Zagórski et al., “Decoding of position in the developing neural tube from antiparallel morphogen gradients,” Science, vol. 356, no. 6345, pp. 1379–1383, 2017.
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2017 | Journal Article | IST-REx-ID: 947 | OA
D. De Martino, F. Capuani, and A. De Martino, “Quantifying the entropic cost of cellular growth control,” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1, 2017.
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2017 | Journal Article | IST-REx-ID: 955 | OA
T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new regulatory functions on biophysically realistic fitness landscapes,” Nature Communications, vol. 8, no. 1, 2017.
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2017 | Journal Article | IST-REx-ID: 959 | OA
D. De Martino, “Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics,” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 95, no. 6, p. 062419, 2017.
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2017 | Journal Article | IST-REx-ID: 993 | OA
A. Levina (Martius) and V. Priesemann, “Subsampling scaling,” Nature Communications, vol. 8, 2017.
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2017 | Journal Article | IST-REx-ID: 1007 | OA
M. Lang and E. Sontag, “Zeros of nonlinear systems with input invariances,” Automatica, vol. 81C, pp. 46–55, 2017.
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2017 | Journal Article | IST-REx-ID: 1104 | OA
S. Deny et al., “Multiplexed computations in retinal ganglion cells of a single type,” Nature Communications, vol. 8, no. 1, 2017.
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2016 | Conference Paper | IST-REx-ID: 8094 | OA
G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Self-organized control of an tendon driven arm by differential extrinsic plasticity,” in Proceedings of the Artificial Life Conference 2016, Cancun, Mexico, 2016, vol. 28, pp. 142–143.
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2016 | Conference Paper | IST-REx-ID: 948
T. Monk, C. Savin, and J. Lücke, “Neurons equipped with intrinsic plasticity learn stimulus intensity statistics,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine, 2016, vol. 29, pp. 4285–4293.
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2016 | Journal Article | IST-REx-ID: 1188 | OA
D. De Martino and D. Masoero, “Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2016, no. 12, 2016.
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2016 | Journal Article | IST-REx-ID: 1197 | OA
J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Error-robust modes of the retinal population code,” PLoS Computational Biology, vol. 12, no. 11, 2016.
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2016 | Journal Article | IST-REx-ID: 1203 | OA
F. Hu et al., “Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination,” Journal of Clinical Microbiology, vol. 54, no. 12, pp. 3010–3017, 2016.
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2016 | Conference Paper | IST-REx-ID: 1214
G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm,” presented at the IEEE RSJ International Conference on Intelligent Robots and Systems IROS , Daejeon, Korea, 2016, vol. 2016–November.
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2016 | Conference Paper | IST-REx-ID: 1220 | OA
G. Mikić, A. Stoll, J. Bevirt, R. Grah, and M. Moore, “Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency,” presented at the AIAA: Aviation Technology, Integration, and Operations Conference, Washington, D.C., USA, 2016, pp. 1–19.
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2016 | Journal Article | IST-REx-ID: 1242 | OA
T. R. Sokolowski, A. Walczak, W. Bialek, and G. Tkacik, “Extending the dynamic range of transcription factor action by translational regulation,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 93, no. 2, 2016.
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2016 | Journal Article | IST-REx-ID: 1244 | OA
P. Recouvreux, T. R. Sokolowski, A. Grammoustianou, P. Tenwolde, and M. Dogterom, “Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells,” PNAS, vol. 113, no. 7, pp. 1811–1816, 2016.
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2016 | Journal Article | IST-REx-ID: 1248 | OA
G. Tkacik and W. Bialek, “Information processing in living systems,” Annual Review of Condensed Matter Physics, vol. 7, pp. 89–117, 2016.
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2016 | Journal Article | IST-REx-ID: 1260 | OA
D. De Martino, “The dual of the space of interactions in neural network models,” International Journal of Modern Physics C, vol. 27, no. 6, p. 1650067, 2016.
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2016 | Journal Article | IST-REx-ID: 1266 | OA
M. J. Chalk, B. Gutkin, and S. Denève, “Neural oscillations as a signature of efficient coding in the presence of synaptic delays,” eLife, vol. 5, no. 2016JULY, 2016.
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2016 | Journal Article | IST-REx-ID: 1270 | OA
P. Hillenbrand, U. Gerland, and G. Tkačik, “Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information,” PLoS One, vol. 11, no. 9, 2016.
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2016 | Journal Article | IST-REx-ID: 1290 | OA
L. Stone, M. Baym, T. Lieberman, R. P. Chait, J. Clardy, and R. Kishony, “Compounds that select against the tetracycline-resistance efflux pump,” Nature Chemical Biology, vol. 12, no. 11, pp. 902–904, 2016.
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2016 | Conference Paper | IST-REx-ID: 1320
M. Lang and E. Sontag, “Scale-invariant systems realize nonlinear differential operators,” presented at the ACC: American Control Conference, Boston, MA, USA, 2016, vol. 2016–July.
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2016 | Journal Article | IST-REx-ID: 1332 | OA
R. P. Chait, A. Palmer, I. Yelin, and R. Kishony, “Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments,” Nature Communications, vol. 7, 2016.
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2016 | Journal Article | IST-REx-ID: 1342 | OA
M. Baym et al., “Spatiotemporal microbial evolution on antibiotic landscapes,” Science, vol. 353, no. 6304, pp. 1147–1151, 2016.
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2016 | Journal Article | IST-REx-ID: 1358 | OA
T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic limits to gene regulation by global crosstalk,” Nature Communications, vol. 7, 2016.
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