Error-robust modes of the retinal population code
J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkadik, M. Berry, PLoS Computational Biology 12 (2016).
LibreCat: https://research-explorer.ista.ac.at/record/1197
DOI: 10.1371/journal.pcbi.1005148

Neurons equipped with intrinsic plasticity learn stimulus intensity statistics
T. Monk, C. Savin, J. Lücke, in:, Neural Information Processing Systems, 2016, pp. 4285–4293.
LibreCat: https://research-explorer.ista.ac.at/record/948

Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information
P. Hillenbrand, U. Gerland, G. Tkadik, PLoS One 11 (2016).
LibreCat: https://research-explorer.ista.ac.at/record/1270
DOI: 10.1371/journal.pone.0163628

Computation of positional information in an Ising model
P. Hillenbrand, U. Gerland, G. Tkadik, (2016).
LibreCat: https://research-explorer.ista.ac.at/record/9870
DOI: 10.1371/journal.pone.0163628.s002

Error bound on an estimator of position
P. Hillenbrand, U. Gerland, G. Tkadik, (2016).
LibreCat: https://research-explorer.ista.ac.at/record/9869
DOI: 10.1371/journal.pone.0163628.s001

Computation of positional information in a discrete morphogen field
P. Hillenbrand, U. Gerland, G. Tkadik, (2016).
LibreCat: https://research-explorer.ista.ac.at/record/9871
DOI: 10.1371/journal.pone.0163628.s003

Studying the complexities of transcriptional regulation
G. Rieckh, Studying the Complexities of Transcriptional Regulation, Institute of Science and Technology Austria, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1128

Intrinsic limits to gene regulation by global crosstalk
T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkadik, Nature Communications 7 (2016).
LibreCat: https://research-explorer.ista.ac.at/record/1358
DOI: 10.1038/ncomms12307

Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study
F. Parise, J. Lygeros, J. Ruess, Frontiers in Environmental Science 3 (2015).
LibreCat: https://research-explorer.ista.ac.at/record/10794
DOI: 10.3389/fenvs.2015.00042

Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space
J. Ruess, Journal of Chemical Physics 143 (2015).
LibreCat: https://research-explorer.ista.ac.at/record/1539
DOI: 10.1063/1.4937937

Iterative experiment design guides the characterization of a light-inducible gene expression circuit
J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, J. Lygeros, PNAS 112 (2015) 8148–8153.
LibreCat: https://research-explorer.ista.ac.at/record/1538
DOI: 10.1073/pnas.1423947112
PMID: 26085136

Editorial: Emergent neural computation from the interaction of different forms of plasticity
M. Gilson, C. Savin, F. Zenke, Frontiers in Computational Neuroscience 9 (2015).
LibreCat: https://research-explorer.ista.ac.at/record/1564
DOI: 10.3389/fncom.2015.00145

Novel plasticity rule can explain the development of sensorimotor intelligence
R. Der, G.S. Martius, PNAS 112 (2015) 24–32.
LibreCat: https://research-explorer.ista.ac.at/record/1570
DOI: 10.1073/pnas.1508400112
PMID: 26504200

Adaptive moment closure for parameter inference of biochemical reaction networks
S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, C. Schilling, 9308 (2015) 77–89.
LibreCat: https://research-explorer.ista.ac.at/record/1658
DOI: 10.1007/978-3-319-23401-4_8

High accuracy decoding of dynamical motion from a large retinal population
O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkadik, M. Berry, PLoS Computational Biology 11 (2015).
LibreCat: https://research-explorer.ista.ac.at/record/1697
DOI: 10.1371/journal.pcbi.1004304

Thermodynamics and signatures of criticality in a network of neurons
G. Tkadik, T. Mora, O. Marre, D. Amodei, S. Palmer, M. Berry Ii, W. Bialek, PNAS 112 (2015) 11508–11513.
LibreCat: https://research-explorer.ista.ac.at/record/1701
DOI: 10.1073/pnas.1514188112
PMID: 26330611

Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks
J. Ruess, J. Lygeros, ACM Transactions on Modeling and Computer Simulation 25 (2015).
LibreCat: https://research-explorer.ista.ac.at/record/1861
DOI: 10.1145/2688906

Positional information, positional error, and readout precision in morphogenesis: A mathematical framework
G. Tkadik, J. Dubuis, M. Petkova, T. Gregor, Genetics 199 (2015) 39–59.
LibreCat: https://research-explorer.ista.ac.at/record/1885
DOI: 10.1534/genetics.114.171850

Optimizing information flow in small genetic networks. IV. Spatial coupling
T.R. Sokolowski, G. Tkadik, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).
LibreCat: https://research-explorer.ista.ac.at/record/1940
DOI: 10.1103/PhysRevE.91.062710

Supporting information text
T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).
LibreCat: https://research-explorer.ista.ac.at/record/9718
DOI: 10.1371/journal.pcbi.1004055.s001

Evolution of bow-tie architectures in biology
T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11 (2015).
LibreCat: https://research-explorer.ista.ac.at/record/1827
DOI: 10.1371/journal.pcbi.1004055

Evolutionary simulation code
T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).
LibreCat: https://research-explorer.ista.ac.at/record/9773
DOI: 10.1371/journal.pcbi.1004055.s002

Other fitness models for comparison & for interacting TFBSs
M. Tugrul, T. Paixao, N.H. Barton, G. Tkadik, (2015).
LibreCat: https://research-explorer.ista.ac.at/record/9712
DOI: 10.1371/journal.pgen.1005639.s001

Dynamics of transcription factor binding site evolution
M. Tugrul, T. Paixao, N.H. Barton, G. Tkadik, PLoS Genetics 11 (2015).
LibreCat: https://research-explorer.ista.ac.at/record/1666
DOI: 10.1371/journal.pgen.1005639

Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation
S.A. Cepeda Humerez, G. Rieckh, G. Tkadik, Physical Review Letters 115 (2015).
LibreCat: https://research-explorer.ista.ac.at/record/1576
DOI: 10.1103/PhysRevLett.115.248101

Quantifying emergent behavior of autonomous robots
G.S. Martius, E. Olbrich, Entropy 17 (2015) 7266–7297.
LibreCat: https://research-explorer.ista.ac.at/record/1655
DOI: 10.3390/e17107266

Spatio-temporal representations of uncertainty in spiking neural networks
C. Savin, S. Denève, in:, Neural Information Processing Systems, 2014, pp. 2024–2032.
LibreCat: https://research-explorer.ista.ac.at/record/1708

Variance predicts salience in central sensory processing
A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, G. Tkadik, ELife (2014).
LibreCat: https://research-explorer.ista.ac.at/record/1886
DOI: 10.7554/eLife.03722

Mathematical model of alternative mechanism of telomere length maintenance
R. Kollár, K. Bodova, J. Nosek, d. Tomáska, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).
LibreCat: https://research-explorer.ista.ac.at/record/1896
DOI: 10.1103/PhysRevE.89.032701

The fitness costs of adaptation via phenotypic plasticity and maternal effects
T. Ezard, R. Prizak, R. Hoyle, Functional Ecology 28 (2014) 693–701.
LibreCat: https://research-explorer.ista.ac.at/record/1909
DOI: 10.1111/1365-2435.12207

Evolutionary dynamics of infectious diseases in finite populations
J. Humplik, A. Hill, M. Nowak, Journal of Theoretical Biology 360 (2014) 149–162.
LibreCat: https://research-explorer.ista.ac.at/record/1928
DOI: 10.1016/j.jtbi.2014.06.039

Emergence of task-dependent representations in working memory circuits
C. Savin, J. Triesch, Frontiers in Computational Neuroscience 8 (2014).
LibreCat: https://research-explorer.ista.ac.at/record/1931
DOI: 10.3389/fncom.2014.00057

Characterizing spiking in noisy type II neurons
K. Bodova, D. Paydarfar, D. Forger,  Journal of Theoretical Biology 365 (2014) 40–54.
LibreCat: https://research-explorer.ista.ac.at/record/2028
DOI: 10.1016/j.jtbi.2014.09.041

Hierarchy and polysynchrony in an adaptive network 
V. Botella Soler, P. Glendinning, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).
LibreCat: https://research-explorer.ista.ac.at/record/2183
DOI: 10.1103/PhysRevE.89.062809

Noise and information transmission in promoters with multiple internal states
G. Rieckh, G. Tkadik, Biophysical Journal 106 (2014) 1194–1204.
LibreCat: https://research-explorer.ista.ac.at/record/2231
DOI: 10.1016/j.bpj.2014.01.014
PMID: 24606943

Adaptation to changes in higher-order stimulus statistics in the salamander retina
G. Tkadik, A. Ghosh, E. Schneidman, R. Segev, PLoS One 9 (2014).
LibreCat: https://research-explorer.ista.ac.at/record/3263
DOI: 10.1371/journal.pone.0085841

Fitness consequences of maternal and grandmaternal effects
R. Prizak, T. Ezard, R. Hoyle, Ecology and Evolution 4 (2014) 3139–3145.
LibreCat: https://research-explorer.ista.ac.at/record/537
DOI: 10.1002/ece3.1150

Data from: Transformation of stimulus correlations by the retina
K. Simmons, J. Prentice, G. Tkadik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, (2014).
LibreCat: https://research-explorer.ista.ac.at/record/9752
DOI: 10.5061/dryad.246qg

Searching for collective behavior in a large network of sensory neurons
G. Tkadik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, M. Berry, PLoS Computational Biology 10 (2014).
LibreCat: https://research-explorer.ista.ac.at/record/2257
DOI: 10.1371/journal.pcbi.1003408

Neuronal oscillations scale up and scale down the brain dynamics 
M. Valderrama, V. Botella Soler, M. Le Van Quyen, in:, M. Meyer, Z. Pesenson (Eds.), Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, Wiley-VCH, 2013.
LibreCat: https://research-explorer.ista.ac.at/record/2413
DOI: 10.1002/9783527671632.ch08

Learning quadratic receptive fields from neural responses to natural stimuli
K. Rajan, O. Marre, G. Tkadik, Neural Computation 25 (2013) 1661–1692.
LibreCat: https://research-explorer.ista.ac.at/record/2818
DOI: 10.1162/NECO_a_00463
arXiv: 1209.0121

The simplest maximum entropy model for collective behavior in a neural network
G. Tkadik, O. Marre, T. Mora, D. Amodei, M. Berry, W. Bialek, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).
LibreCat: https://research-explorer.ista.ac.at/record/2850
DOI: 10.1088/1742-5468/2013/03/P03011
arXiv: 1207.6319

A simple method for estimating the entropy of neural activity
M. Berry, G. Tkadik, J. Dubuis, O. Marre, R. Da Silveira, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).
LibreCat: https://research-explorer.ista.ac.at/record/2851
DOI: 10.1088/1742-5468/2013/03/P03015

Stimulus-dependent maximum entropy models of neural population codes
E. Granot Atedgi, G. Tkadik, R. Segev, E. Schneidman, PLoS Computational Biology 9 (2013).
LibreCat: https://research-explorer.ista.ac.at/record/2863
DOI: 10.1371/journal.pcbi.1002922

Lyapunov exponent and topological entropy plateaus in piecewise linear maps
V. Botella Soler, J. Oteo, J. Ros, P. Glendinning, Journal of Physics A: Mathematical and Theoretical 46 (2013).
LibreCat: https://research-explorer.ista.ac.at/record/2861
DOI: 10.1088/1751-8113/46/12/125101

Retinal metric: a stimulus distance measure derived from population neural responses
G. Tkadik, E. Granot Atedgi, R. Segev, E. Schneidman, Physical Review Letters 110 (2013).
LibreCat: https://research-explorer.ista.ac.at/record/2913
DOI: 10.1103/PhysRevLett.110.058104

Positional information, in bits
J. Dubuis, G. Tkadik, E. Wieschaus, T. Gregor, W. Bialek, PNAS 110 (2013) 16301–16308.
LibreCat: https://research-explorer.ista.ac.at/record/3261
DOI: 10.1073/pnas.1315642110
PMID: 24089448

Dynamic persistence of antibiotic-stressed mycobacteria
Y. Wakamoto, N. Dhar, R.P. Chait, K. Schneider, F. Signorino Gelo, S. Leibler, J. Mckinney, Science 339 (2013) 91–95.
LibreCat: https://research-explorer.ista.ac.at/record/499
DOI: 10.1126/science.1229858

Transformation of stimulus correlations by the retina
K. Simmons, J. Prentice, G. Tkadik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, PLoS Computational Biology 9 (2013).
LibreCat: https://research-explorer.ista.ac.at/record/2277
DOI: 10.1371/journal.pcbi.1003344

Statistical thermodynamics of natural images
G. Stephens, T. Mora, G. Tkadik, W. Bialek, Physical Review Letters 110 (2013).
LibreCat: https://research-explorer.ista.ac.at/record/2914
DOI: 10.1103/PhysRevLett.110.018701
arXiv: 0806.2694