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.
LibreCat: https://research-explorer.ista.ac.at/record/735
DOI: 10.1016/j.devcel.2017.09.014
WoS: 000413443700011

Relevant sparse codes with variational information bottleneck
M.J. Chalk, O. Marre, G. Tkadik, in:, Neural Information Processing Systems, 2016, pp. 1965–1973.
LibreCat: https://research-explorer.ista.ac.at/record/1082

Estimating nonlinear neural response functions using GP priors and Kronecker methods
C. Savin, G. Tkadik, in:, Neural Information Processing Systems, 2016, pp. 3610–3618.
LibreCat: https://research-explorer.ista.ac.at/record/1105

Modular parameter identification of biomolecular networks
M. Lang, J. Stelling, SIAM Journal on Scientific Computing 38 (2016) 8–08.
LibreCat: https://research-explorer.ista.ac.at/record/1170
DOI: 10.1137/15M103306X

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.
LibreCat: https://research-explorer.ista.ac.at/record/1171
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.
LibreCat: https://research-explorer.ista.ac.at/record/1203
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.
LibreCat: https://research-explorer.ista.ac.at/record/1214
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.
LibreCat: https://research-explorer.ista.ac.at/record/1244
DOI: 10.1073/pnas.1419248113

Information processing in living systems
G. Tkadik, W. Bialek, Annual Review of Condensed Matter Physics 7 (2016) 89–117.
LibreCat: https://research-explorer.ista.ac.at/record/1248
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).
LibreCat: https://research-explorer.ista.ac.at/record/1266
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.
LibreCat: https://research-explorer.ista.ac.at/record/1290
DOI: 10.1038/nchembio.2176

Scale-invariant systems realize nonlinear differential operators
M. Lang, E. Sontag, in:, IEEE, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1320
DOI: 10.1109/ACC.2016.7526722

Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments
R.P. Chait, A. Palmer, I. Yelin, R. Kishony, Nature Communications 7 (2016).
LibreCat: https://research-explorer.ista.ac.at/record/1332
DOI: 10.1038/ncomms10333

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.
LibreCat: https://research-explorer.ista.ac.at/record/1342
DOI: 10.1126/science.aag0822

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).
LibreCat: https://research-explorer.ista.ac.at/record/1394
DOI: 10.1088/1478-3975/13/3/036005

A general approximation for the dynamics of quantitative traits
K. Bodova, G. Tkadik, N.H. Barton, Genetics 202 (2016) 1523–1548.
LibreCat: https://research-explorer.ista.ac.at/record/1420
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).
LibreCat: https://research-explorer.ista.ac.at/record/1485
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.
LibreCat: https://research-explorer.ista.ac.at/record/1148
DOI: 10.1016/j.biosystems.2016.07.005

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.
LibreCat: https://research-explorer.ista.ac.at/record/8094
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).
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