Limiting shapes of confined lipid vesicles
B. Kavcic, A. Sakashita, H. Noguchi, P. Ziherl, Soft Matter 15 (2019) 602–614.
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Estimating information flow in single cells
S.A. Cepeda Humerez, Estimating Information Flow in Single Cells, Institute of Science and Technology Austria, 2019.
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Coevolution of transcription factors and their binding sites in sequence space
R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in Sequence Space, Institute of Science and Technology Austria, 2019.
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Non-equilibrium critical dynamics of bursts in ;8 and ;4 rhythms as fundamental characteristic of sleep and wake micro-architecture
J.W.J.L. Wang, F. Lombardi, X. Zhang, C. Anaclet, P.C. Ivanov, PLoS Computational Biology 15 (2019).
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Receptor crosstalk improves concentration sensing of multiple ligands
M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G. Reddy, I. Nemenman, T. Mora, Physical Review E 99 (2019).
LibreCat: https://research-explorer.ista.ac.at/record/6090
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A tight upper bound on mutual information
M. Hledik, T.R. Sokolowski, G. Tkadik, in:, IEEE Information Theory Workshop, ITW 2019, IEEE, 2019.
LibreCat: https://research-explorer.ista.ac.at/record/7606
DOI: 10.1109/ITW44776.2019.8989292
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arXiv: 1812.01475

An introduction to the maximum entropy approach and its application to inference problems in biology
A. De Martino, D. De Martino, Heliyon 4 (2018).
LibreCat: https://research-explorer.ista.ac.at/record/306
DOI: 10.1016/j.heliyon.2018.e00596

Fabrication and operation of microfluidic hanging drop networks
P. Misun, A. Birchler, M. Lang, A. Hierlemann, O. Frey, Methods in Molecular Biology 1771 (2018) 183–202.
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Distributed and dynamic intracellular organization of extracellular information
A. Granados, J. Pietsch, S.A. Cepeda Humerez, I. Farquhar, G. Tkadik, P. Swain, PNAS 115 (2018) 6088–6093.
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DOI: 10.1073/pnas.1716659115
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Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system
K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, Genetics 209 (2018) 861–883.
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Supplemental material for Bodova et al., 2018
K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018).
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Probabilistic models of individual and collective animal behavior
K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkadik, PLoS One 13 (2018).
LibreCat: https://research-explorer.ista.ac.at/record/406
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Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity
M. Pleska, M. Lang, D. Refardt, B. Levin, C.C. Guet, Nature Ecology and Evolution 2 (2018) 359–366.
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Implementation of the inference method in Matlab
K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkadik, (2018).
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Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons
U. Ferrari, S. Deny, M.J. Chalk, G. Tkadik, O. Marre, T. Mora, Physical Review E 98 (2018).
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Toward a unified theory of efficient, predictive, and sparse coding
M.J. Chalk, O. Marre, G. Tkadik, PNAS 115 (2018) 186–191.
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Well posedness and maximum entropy approximation for the dynamics of quantitative traits
K. Bodova, J. Haskovec, P. Markowich, Physica D: Nonlinear Phenomena 376–377 (2018) 108–120.
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Nonoptimal gene expression creates latent potential for antibiotic resistance
A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018) 2669–2684.
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Nonlinear decoding of a complex movie from the mammalian retina
V. Botella Soler, S. Deny, G.S. Martius, O. Marre, G. Tkadik, PLoS Computational Biology 14 (2018).
LibreCat: https://research-explorer.ista.ac.at/record/292
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Statistical mechanics for metabolic networks during steady state growth
D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkadik, Nature Communications 9 (2018).
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Evolutionary potential of transcription factors for gene regulatory rewiring
C. Igler, M. Lagator, G. Tkadik, J.P. Bollback, C.C. Guet, Nature Ecology and Evolution 2 (2018) 1633–1643.
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Shaping bacterial population behavior through computer interfaced control of individual cells
R.P. Chait, J. Ruess, T. Bergmiller, G. Tkadik, C.C. Guet, Nature Communications 8 (2017).
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Dynamical self consistency leads to behavioral development and emergent social interactions in robots
R. Der, G.S. Martius, in:, IEEE, 2017.
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Self organized behavior generation for musculoskeletal robots
R. Der, G.S. Martius, Frontiers in Neurorobotics 11 (2017).
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Probabilistic models for neural populations that naturally capture global coupling and criticality
J. Humplik, G. Tkadik, PLoS Computational Biology 13 (2017).
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Discrete modes of social information processing predict individual behavior of fish in a group
R. Harpaz, G. Tkadik, E. Schneidman, PNAS 114 (2017) 10149–10154.
LibreCat: https://research-explorer.ista.ac.at/record/725
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PMID: 28874581

Data from: Error-robust modes of the retinal population code
J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkadik, M. Berry, (2017).
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Sensory noise predicts divisive reshaping of receptive fields
M.J. Chalk, P. Masset, B. Gutkin, S. Denève, PLoS Computational Biology 13 (2017).
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Supplementary appendix
M.J. Chalk, P. Masset, B. Gutkin, S. Denève, (2017).
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Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment
K. Mitosch, G. Rieckh, M.T. Bollenbach, Cell Systems 4 (2017) 393–403.
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Exact goodness-of-fit testing for the Ising model
A. Martin Del Campo Sanchez, S.A. Cepeda Humerez, C. Uhler, Scandinavian Journal of Statistics 44 (2017) 285–306.
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Multiplexed computations in retinal ganglion cells of a single type
S. Deny, U. Ferrari, E. Mace, P. Yger, R. Caplette, S. Picaud, G. Tkadik, O. Marre, Nature Communications 8 (2017).
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Subsampling scaling
A. Levina (Martius), V. Priesemann, Nature Communications 8 (2017).
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Evolution of new regulatory functions on biophysically realistic fitness landscapes
T. Friedlander, R. Prizak, N.H. Barton, G. Tkadik, Nature Communications 8 (2017).
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Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics
D. De Martino,  Physical Review E Statistical Nonlinear and Soft Matter Physics  95 (2017) 062419.
LibreCat: https://research-explorer.ista.ac.at/record/959
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Quantifying the entropic cost of cellular growth control
D. De Martino, F. Capuani, A. De Martino,  Physical Review E Statistical Nonlinear and Soft Matter Physics  96 (2017).
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Decoding of position in the developing neural tube from antiparallel morphogen gradients
M.P. Zagórski, Y. Tabata, N. Brandenberg, M. Lutolf, G. Tkadik, T. Bollenbach, J. Briscoe, A. Kicheva, Science 356 (2017) 1379–1383.
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Phase transitions in integer linear problems
S. Colabrese, D. De Martino, L. Leuzzi, E. Marinari,  Journal of Statistical Mechanics: Theory and Experiment 2017 (2017).
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Maximum entropy models as a tool for building precise neural controls
C. Savin, G. Tkadik, Current Opinion in Neurobiology 46 (2017) 120–126.
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Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes
D. De Martino, Physical Review E 96 (2017).
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Zeros of nonlinear systems with input invariances
M. Lang, E. Sontag, Automatica 81C (2017) 46–55.
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Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity
T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild, G. Tkadik, C.C. Guet, Science 356 (2017) 311–315.
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An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate
V. Barone, M. Lang, G. Krens, S. Pradhan, S. Shamipour, K. Sako, M.K. Sikora, C.C. Guet, C.-P.J. Heisenberg, Developmental Cell 43 (2017) 198–211.
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Relevant sparse codes with variational information bottleneck
M.J. Chalk, O. Marre, G. Tkadik, in:, Neural Information Processing Systems, 2016, pp. 1965–1973.
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Estimating nonlinear neural response functions using GP priors and Kronecker methods
C. Savin, G. Tkadik, in:, Neural Information Processing Systems, 2016, pp. 3610–3618.
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Modular parameter identification of biomolecular networks
M. Lang, J. Stelling, SIAM Journal on Scientific Computing 38 (2016) 8–08.
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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.
G. Tkadik, Physics of Life Reviews 17 (2016) 166–167.
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DOI: 10.1016/j.plrev.2016.06.005

Asymptotic analysis of noisy fitness maximization, applied to metabolism &amp; growth
D. De Martino, D. Masoero,  Journal of Statistical Mechanics: Theory and Experiment 2016 (2016).
LibreCat: https://research-explorer.ista.ac.at/record/1188
DOI: 10.1088/1742-5468/aa4e8f

Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination
F. Hu, L. Rishishwar, A. Sivadas, G. Mitchell, J. King, T. Murphy, J. Gilsdorf, L. Mayer, X. Wang, Journal of Clinical Microbiology 54 (2016) 3010–3017.
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DOI: 10.1128/JCM.01511-16

Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm
G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, IEEE, 2016.
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DOI: 10.1109/IROS.2016.7759138

Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency
G. Miki, A. Stoll, J. Bevirt, R. Grah, M. Moore, in:, AIAA, 2016, pp. 1–19.
LibreCat: https://research-explorer.ista.ac.at/record/1220
DOI: 10.2514/6.2016-3764

Extending the dynamic range of transcription factor action by translational regulation
T.R. Sokolowski, A. Walczak, W. Bialek, G. Tkadik, Physical Review E Statistical Nonlinear and Soft Matter Physics 93 (2016).
LibreCat: https://research-explorer.ista.ac.at/record/1242
DOI: 10.1103/PhysRevE.93.022404

Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells
P. Recouvreux, T.R. Sokolowski, A. Grammoustianou, P. Tenwolde, M. Dogterom, PNAS 113 (2016) 1811–1816.
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Information processing in living systems
G. Tkadik, W. Bialek, Annual Review of Condensed Matter Physics 7 (2016) 89–117.
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DOI: 10.1146/annurev-conmatphys-031214-014803

The dual of the space of interactions in neural network models
D. De Martino, International Journal of Modern Physics C 27 (2016).
LibreCat: https://research-explorer.ista.ac.at/record/1260
DOI: 10.1142/S0129183116500674
arXiv: 1505.02963

Neural oscillations as a signature of efficient coding in the presence of synaptic delays
M.J. Chalk, B. Gutkin, S. Denève, ELife 5 (2016).
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DOI: 10.7554/eLife.13824

Compounds that select against the tetracycline-resistance efflux pump
L. Stone, M. Baym, T. Lieberman, R.P. Chait, J. Clardy, R. Kishony, Nature Chemical Biology 12 (2016) 902–904.
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Scale-invariant systems realize nonlinear differential operators
M. Lang, E. Sontag, in:, IEEE, 2016.
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Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments
R.P. Chait, A. Palmer, I. Yelin, R. Kishony, Nature Communications 7 (2016).
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Spatiotemporal microbial evolution on antibiotic landscapes
M. Baym, T. Lieberman, E. Kelsic, R.P. Chait, R. Gross, I. Yelin, R. Kishony, Science 353 (2016) 1147–1151.
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Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli
D. De Martino, F. Capuani, A. De Martino, Physical Biology 13 (2016).
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A general approximation for the dynamics of quantitative traits
K. Bodova, G. Tkadik, N.H. Barton, Genetics 202 (2016) 1523–1548.
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DOI: 10.1534/genetics.115.184127
arXiv: 1510.08344

Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis
D. De Martino, Physical Biology 13 (2016).
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DOI: 10.1088/1478-3975/13/1/016003

Adaptive moment closure for parameter inference of biochemical reaction networks
C. Schilling, S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, Biosystems 149 (2016) 15–25.
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Self-organized control of an tendon driven arm by differential extrinsic plasticity
G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, Proceedings of the Artificial Life Conference 2016, MIT Press, 2016, pp. 142–143.
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DOI: 10.7551/978-0-262-33936-0-ch029

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).
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Neurons equipped with intrinsic plasticity learn stimulus intensity statistics
T. Monk, C. Savin, J. Lücke, in:, Neural Information Processing Systems, 2016, pp. 4285–4293.
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Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information
P. Hillenbrand, U. Gerland, G. Tkadik, PLoS One 11 (2016).
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DOI: 10.1371/journal.pone.0163628

Computation of positional information in an Ising model
P. Hillenbrand, U. Gerland, G. Tkadik, (2016).
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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).
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Studying the complexities of transcriptional regulation
G. Rieckh, Studying the Complexities of Transcriptional Regulation, Institute of Science and Technology Austria, 2016.
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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
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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).
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Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space
J. Ruess, Journal of Chemical Physics 143 (2015).
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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.
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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).
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Novel plasticity rule can explain the development of sensorimotor intelligence
R. Der, G.S. Martius, PNAS 112 (2015) 24–32.
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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.
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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).
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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.
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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).
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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.
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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
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Evolution of bow-tie architectures in biology
T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11 (2015).
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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