Please note that IST Research Explorer no longer supports Internet Explorer versions 8 or 9 (or earlier).

We recommend upgrading to the latest Internet Explorer, Google Chrome, or Firefox.

159 Publications


2016 | Journal Article | IST-REx-ID: 1171
Tkačik, G. (2016). Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O. C. Martin et al. Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.06.005
View | DOI
 

2016 | Journal Article | IST-REx-ID: 1188 | OA
De Martino, D., & Masoero, D. (2016). Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth. Journal of Statistical Mechanics: Theory and Experiment. IOPscience. https://doi.org/10.1088/1742-5468/aa4e8f
View | DOI | Download Preprint (ext.)
 

2016 | Journal Article | IST-REx-ID: 1203 | OA
Hu, F., Rishishwar, L., Sivadas, A., Mitchell, G., King, J., Murphy, T., … Wang, X. (2016). Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. Journal of Clinical Microbiology. American Society for Microbiology. https://doi.org/10.1128/JCM.01511-16
View | DOI | Download Submitted Version (ext.)
 

2016 | Conference Paper | IST-REx-ID: 1214
Martius, G. S., Hostettler, R., Knoll, A., & Der, R. (2016). Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm (Vol. 2016–November). Presented at the IEEE RSJ International Conference on Intelligent Robots and Systems IROS , Daejeon, Korea: IEEE. https://doi.org/10.1109/IROS.2016.7759138
View | DOI
 

2016 | Conference Paper | IST-REx-ID: 1220 | OA
Mikić, G., Stoll, A., Bevirt, J., Grah, R., & Moore, M. (2016). Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency (pp. 1–19). Presented at the AIAA: Aviation Technology, Integration, and Operations Conference, Washington, D.C., USA: AIAA. https://doi.org/10.2514/6.2016-3764
View | DOI | Download Preprint (ext.)
 

2016 | Journal Article | IST-REx-ID: 1242 | OA
Sokolowski, T. R., Walczak, A., Bialek, W., & Tkačik, G. (2016). Extending the dynamic range of transcription factor action by translational regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.93.022404
View | DOI | Download Preprint (ext.)
 

2016 | Journal Article | IST-REx-ID: 1244 | OA
Recouvreux, P., Sokolowski, T. R., Grammoustianou, A., Tenwolde, P., & Dogterom, M. (2016). Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1419248113
View | DOI | Download Submitted Version (ext.)
 

2016 | Journal Article | IST-REx-ID: 1248 | OA
Tkačik, G., & Bialek, W. (2016). Information processing in living systems. Annual Review of Condensed Matter Physics. Annual Reviews. https://doi.org/10.1146/annurev-conmatphys-031214-014803
View | DOI | Download Preprint (ext.)
 

2016 | Journal Article | IST-REx-ID: 1260 | OA
De Martino, D. (2016). The dual of the space of interactions in neural network models. International Journal of Modern Physics C. World Scientific Publishing. https://doi.org/10.1142/S0129183116500674
View | DOI | Download Preprint (ext.) | arXiv
 

2016 | Journal Article | IST-REx-ID: 1266 | OA
Chalk, M. J., Gutkin, B., & Denève, S. (2016). Neural oscillations as a signature of efficient coding in the presence of synaptic delays. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.13824
View | Files available | DOI
 

2016 | Conference Paper | IST-REx-ID: 948
Monk, T., Savin, C., & Lücke, J. (2016). Neurons equipped with intrinsic plasticity learn stimulus intensity statistics (Vol. 29, pp. 4285–4293). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine: Neural Information Processing Systems.
View | Download None (ext.)
 

2016 | Journal Article | IST-REx-ID: 1197 | OA
Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M. (2016). Error-robust modes of the retinal population code. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005148
View | Files available | DOI
 

2016 | Journal Article | IST-REx-ID: 1270 | OA
Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628
View | Files available | DOI
 

2016 | Research Data Reference | IST-REx-ID: 9870
Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Computation of positional information in an Ising model. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628.s002
View | Files available | DOI
 

2016 | Research Data Reference | IST-REx-ID: 9869
Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Error bound on an estimator of position. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628.s001
View | Files available | DOI
 

2016 | Research Data Reference | IST-REx-ID: 9871
Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Computation of positional information in a discrete morphogen field. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628.s003
View | Files available | DOI
 

2015 | Journal Article | IST-REx-ID: 1697 | OA
Marre, O., Botella Soler, V., Simmons, K., Mora, T., Tkačik, G., & Berry, M. (2015). High accuracy decoding of dynamical motion from a large retinal population. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004304
View | Files available | DOI
 

2015 | Journal Article | IST-REx-ID: 1701 | OA
Tkačik, G., Mora, T., Marre, O., Amodei, D., Palmer, S., Berry Ii, M., & Bialek, W. (2015). Thermodynamics and signatures of criticality in a network of neurons. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1514188112
View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 

2015 | Journal Article | IST-REx-ID: 1861
Ruess, J., & Lygeros, J. (2015). Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. ACM Transactions on Modeling and Computer Simulation. ACM. https://doi.org/10.1145/2688906
View | DOI
 

2015 | Journal Article | IST-REx-ID: 1885 | OA
Tkačik, G., Dubuis, J., Petkova, M., & Gregor, T. (2015). Positional information, positional error, and readout precision in morphogenesis: A mathematical framework. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.114.171850
View | DOI | Download Preprint (ext.)
 

2015 | Journal Article | IST-REx-ID: 1940 | OA
Sokolowski, T. R., & Tkačik, G. (2015). Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.91.062710
View | DOI | Download Preprint (ext.)
 

2015 | Journal Article | IST-REx-ID: 1538 | OA
Ruess, J., Parise, F., Milias Argeitis, A., Khammash, M., & Lygeros, J. (2015). Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1423947112
View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 

2015 | Journal Article | IST-REx-ID: 1539 | OA
Ruess, J. (2015). Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. American Institute of Physics. https://doi.org/10.1063/1.4937937
View | Files available | DOI
 

2015 | Journal Article | IST-REx-ID: 1564 | OA
Gilson, M., Savin, C., & Zenke, F. (2015). Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncom.2015.00145
View | Files available | DOI
 

2015 | Journal Article | IST-REx-ID: 1570 | OA
Der, R., & Martius, G. S. (2015). Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1508400112
View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 

2015 | Journal Article | IST-REx-ID: 1576 | OA
Cepeda Humerez, S. A., Rieckh, G., & Tkačik, G. (2015). Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.115.248101
View | Files available | DOI | Download Preprint (ext.)
 

2015 | Journal Article | IST-REx-ID: 1655 | OA
Martius, G. S., & Olbrich, E. (2015). Quantifying emergent behavior of autonomous robots. Entropy. Multidisciplinary Digital Publishing Institute. https://doi.org/10.3390/e17107266
View | Files available | DOI
 

2015 | Conference Paper | IST-REx-ID: 1658
Bogomolov, S., Henzinger, T. A., Podelski, A., Ruess, J., & Schilling, C. (2015). Adaptive moment closure for parameter inference of biochemical reaction networks. Presented at the CMSB: Computational Methods in Systems Biology, Nantes, France: Springer. https://doi.org/10.1007/978-3-319-23401-4_8
View | Files available | DOI
 

2015 | Journal Article | IST-REx-ID: 1666 | OA
Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Dynamics of transcription factor binding site evolution. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005639
View | Files available | DOI
 

2015 | Research Data Reference | IST-REx-ID: 9712
Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Other fitness models for comparison & for interacting TFBSs. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005639.s001
View | Files available | DOI
 

2015 | Research Data Reference | IST-REx-ID: 9718
Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Supporting information text. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s001
View | Files available | DOI
 

2015 | Journal Article | IST-REx-ID: 1827 | OA
Friedlander, T., Mayo, A., Tlusty, T., & Alon, U. (2015). Evolution of bow-tie architectures in biology. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055
View | Files available | DOI
 

2015 | Research Data Reference | IST-REx-ID: 9773
Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Evolutionary simulation code. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s002
View | Files available | DOI
 

2014 | Conference Paper | IST-REx-ID: 1708
Savin, C., & Denève, S. (2014). Spatio-temporal representations of uncertainty in spiking neural networks (Vol. 3, pp. 2024–2032). Presented at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information Processing Systems.
View | Download None (ext.)
 

2014 | Journal Article | IST-REx-ID: 1886 | OA
Hermundstad, A., Briguglio, J., Conte, M., Victor, J., Balasubramanian, V., & Tkačik, G. (2014). Variance predicts salience in central sensory processing. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.03722
View | Files available | DOI
 

2014 | Journal Article | IST-REx-ID: 1896 | OA
Kollár, R., Bod’ová, K., Nosek, J., & Tomáška, Ľ. (2014). Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.89.032701
View | DOI | Download Submitted Version (ext.)
 

2014 | Journal Article | IST-REx-ID: 1909 | OA
Ezard, T., Prizak, R., & Hoyle, R. (2014). The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. Wiley-Blackwell. https://doi.org/10.1111/1365-2435.12207
View | Files available | DOI
 

2014 | Journal Article | IST-REx-ID: 1928
Humplik, J., Hill, A., & Nowak, M. (2014). Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2014.06.039
View | DOI
 

2014 | Journal Article | IST-REx-ID: 1931 | OA
Savin, C., & Triesch, J. (2014). Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncom.2014.00057
View | DOI | Download Submitted Version (ext.)
 

2014 | Journal Article | IST-REx-ID: 2231 | OA
Rieckh, G., & Tkačik, G. (2014). Noise and information transmission in promoters with multiple internal states. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2014.01.014
View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 

2014 | Journal Article | IST-REx-ID: 2257 | OA
Tkačik, G., Marre, O., Amodei, D., Schneidman, E., Bialek, W., & Berry, M. (2014). Searching for collective behavior in a large network of sensory neurons. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1003408
View | Files available | DOI | Download Published Version (ext.)
 

2014 | Journal Article | IST-REx-ID: 537 | OA
Prizak, R., Ezard, T., & Hoyle, R. (2014). Fitness consequences of maternal and grandmaternal effects. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.1150
View | Files available | DOI
 

2014 | Journal Article | IST-REx-ID: 3263 | OA
Tkačik, G., Ghosh, A., Schneidman, E., & Segev, R. (2014). Adaptation to changes in higher-order stimulus statistics in the salamander retina. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0085841
View | Files available | DOI
 

2014 | Research Data Reference | IST-REx-ID: 9752
Simmons, K., Prentice, J., Tkačik, G., Homann, J., Yee, H., Palmer, S., … Balasubramanian, V. (2014). Data from: Transformation of stimulus correlations by the retina. Dryad. https://doi.org/10.5061/dryad.246qg
View | Files available | DOI
 

2013 | Book Chapter | IST-REx-ID: 2413
Valderrama, M., Botella Soler, V., & Le Van Quyen, M. (2013). Neuronal oscillations scale up and scale down the brain dynamics . In M. Meyer & Z. Pesenson (Eds.), Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain. Wiley-VCH. https://doi.org/10.1002/9783527671632.ch08
View | DOI
 

2013 | Journal Article | IST-REx-ID: 2818 | OA
Rajan, K., Marre, O., & Tkačik, G. (2013). Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation. MIT Press . https://doi.org/10.1162/NECO_a_00463
View | DOI | Download Preprint (ext.) | arXiv
 

2013 | Journal Article | IST-REx-ID: 2850 | OA
Tkačik, G., Marre, O., Mora, T., Amodei, D., Berry, M., & Bialek, W. (2013). The simplest maximum entropy model for collective behavior in a neural network. Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd. https://doi.org/10.1088/1742-5468/2013/03/P03011
View | DOI | Download Preprint (ext.) | arXiv
 

2013 | Journal Article | IST-REx-ID: 2851
Berry, M., Tkačik, G., Dubuis, J., Marre, O., & Da Silveira, R. (2013). A simple method for estimating the entropy of neural activity. Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd. https://doi.org/10.1088/1742-5468/2013/03/P03015
View | DOI
 

2013 | Journal Article | IST-REx-ID: 2861
Botella Soler, V., Oteo, J., Ros, J., & Glendinning, P. (2013). Lyapunov exponent and topological entropy plateaus in piecewise linear maps. Journal of Physics A: Mathematical and Theoretical. IOP Publishing Ltd. https://doi.org/10.1088/1751-8113/46/12/125101
View | DOI
 

2013 | Journal Article | IST-REx-ID: 2863 | OA
Granot Atedgi, E., Tkačik, G., Segev, R., & Schneidman, E. (2013). Stimulus-dependent maximum entropy models of neural population codes. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1002922
View | Files available | DOI
 

Filters and Search Terms

department=GaTk

Search

Filter Publications