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Gasper Tkacik

Rok Grah

Bor Kavcic

Moritz Lang

Aditya Gilra

Mantas Gabrielaitis

Michal Hledik

Fabrizio Lombardi

Wiktor Mlynarski

Gabriel Mitchell

Tamar Friedlander

Jan Humplik

Remy Chait

Thomas Sokolowski

Georg Rieckh

Vicent Botella Soler

Jakob Ruess

Georg Martius

Roshan Prizak

Anna Levina (Martius)

Katarina Bodova

Daniele De Martino

Cristina Savin

Anna Andersson

Matthew Chalk

Sarah Cepeda Humerez



114 Publications

2017 | Journal Article | IST-REx-ID: 1104   OA
Multiplexed computations in retinal ganglion cells of a single type
S. Deny, U. Ferrari, E. Mace, P. Yger, R. Caplette, S. Picaud, G. Tkacik, O. Marre, Nature Communications 8 (2017) 1964.
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2017 | Journal Article | IST-REx-ID: 548   OA
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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2017 | Journal Article | IST-REx-ID: 613   OA
Shaping bacterial population behavior through computer interfaced control of individual cells
R.P. Chait, J. Ruess, T. Bergmiller, G. Tkacik, C.C. Guet, Nature Communications 8 (2017).
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2017 | Journal Article | IST-REx-ID: 947   OA
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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2017 | Journal Article | IST-REx-ID: 959   OA
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.
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2017 | Conference Paper | IST-REx-ID: 652
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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2017 | Journal Article | IST-REx-ID: 823   OA
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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2017 | Journal Article | IST-REx-ID: 943   OA
Decoding of position in the developing neural tube from antiparallel morphogen gradients
M.P. Zagórski, Y. Tabata, N. Brandenberg, M. Lutolf, G. Tkacik, T. Bollenbach, J. Briscoe, A. Kicheva, Science 356 (2017) 1379–1383.
View | DOI | Download (ext.) | PubMed | Europe PMC
 
2017 | Journal Article | IST-REx-ID: 955   OA
Evolution of new regulatory functions on biophysically realistic fitness landscapes
T. Friedlander, R. Prizak, N.H. Barton, G. Tkacik, Nature Communications 8 (2017) 216.
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2017 | Journal Article | IST-REx-ID: 993   OA
Subsampling scaling
A. Levina (Martius), V. Priesemann, Nature Communications 8 (2017).
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2017 | Journal Article | IST-REx-ID: 2016
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.
View | Files available | DOI | Download (ext.) | arXiv
 
2017 | Research Data | IST-REx-ID: 5560
Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity
T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild, G. Tkacik, C.C. Guet, Biased Partitioning of the Multi-Drug Efflux Pump AcrAB-TolC Underlies Long-Lived Phenotypic Heterogeneity, IST Austria, 2017.
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2017 | Journal Article | IST-REx-ID: 665
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. Tkacik, C.C. Guet, Science 356 (2017) 311–315.
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2017 | Journal Article | IST-REx-ID: 730
Maximum entropy models as a tool for building precise neural controls
C. Savin, G. Tkacik, Current Opinion in Neurobiology 46 (2017) 120–126.
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2017 | Journal Article | IST-REx-ID: 735
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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2017 | Journal Article | IST-REx-ID: 658   OA
Self organized behavior generation for musculoskeletal robots
R. Der, G.S. Martius, Frontiers in Neurorobotics 11 (2017) 00008.
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2017 | Journal Article | IST-REx-ID: 1007   OA
Zeros of nonlinear systems with input invariances
M. Lang, E. Sontag, Automatica 81C (2017) 46–55.
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2017 | Journal Article | IST-REx-ID: 680   OA
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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2017 | Journal Article | IST-REx-ID: 666
Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment
K. Mitosch, G. Rieckh, T. Bollenbach, Cell Systems 4 (2017) 393–403.
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2016 | Thesis | IST-REx-ID: 1128
Studying the complexities of transcriptional regulation
G. Rieckh, Studying the Complexities of Transcriptional Regulation, IST Austria, 2016.
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2016 | Journal Article | IST-REx-ID: 1197   OA
Error-robust modes of the retinal population code
J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkacik, M. Berry, PLoS Computational Biology 12 (2016).
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2016 | Journal Article | IST-REx-ID: 1248   OA
Information processing in living systems
G. Tkacik, W. Bialek, Annual Review of Condensed Matter Physics 7 (2016) 89–117.
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2016 | Journal Article | IST-REx-ID: 1332   OA
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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2016 | Conference Paper | IST-REx-ID: 1320
Scale-invariant systems realize nonlinear differential operators
M. Lang, E. Sontag, in:, IEEE, 2016.
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2016 | Journal Article | IST-REx-ID: 1394   OA
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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2016 | Conference Paper | IST-REx-ID: 1105
Estimating nonlinear neural response functions using GP priors and Kronecker methods
C. Savin, G. Tkacik, in:, Neural Information Processing Systems, 2016, pp. 3610–3618.
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2016 | Conference Paper | IST-REx-ID: 1220   OA
Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency
G. Mikić, A. Stoll, J. Bevirt, R. Grah, M. Moore, in:, AIAA, 2016, pp. 1–19.
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2016 | Journal Article | IST-REx-ID: 1270   OA
Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information
P. Hillenbrand, U. Gerland, G. Tkacik, PLoS One 11 (2016).
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2016 | Journal Article | IST-REx-ID: 1244   OA
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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2016 | Journal Article | IST-REx-ID: 1148
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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2016 | Journal Article | IST-REx-ID: 1170
Modular parameter identification of biomolecular networks
M. Lang, J. Stelling, SIAM Journal on Scientific Computing 38 (2016) B988–B1008.
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2016 | Conference Paper | IST-REx-ID: 1214
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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2016 | Journal Article | IST-REx-ID: 1290   OA
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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2016 | Journal Article | IST-REx-ID: 1485   OA
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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2016 | Journal Article | IST-REx-ID: 1358
Intrinsic limits to gene regulation by global crosstalk
T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkacik, Nature Communications 7 (2016) 12307.
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2016 | Conference Paper | IST-REx-ID: 948
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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2016 | Conference Paper | IST-REx-ID: 1082   OA
Relevant sparse codes with variational information bottleneck
M.J. Chalk, O. Marre, G. Tkacik, in:, Neural Information Processing Systems, 2016, pp. 1965–1973.
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2016 | Journal Article | IST-REx-ID: 1171
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.
G. Tkacik, Physics of Life Reviews 17 (2016) 166–167.
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2016 | Journal Article | IST-REx-ID: 1188   OA
Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth
D. De Martino, D. Masoero, Journal of Statistical Mechanics: Theory and Experiment 2016 (2016) 123502.
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2016 | Journal Article | IST-REx-ID: 1203   OA
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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2016 | Journal Article | IST-REx-ID: 1260   OA
The dual of the space of interactions in neural network models
D. De Martino, International Journal of Modern Physics C 27 (2016).
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2016 | Journal Article | IST-REx-ID: 1342   OA
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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2016 | Journal Article | IST-REx-ID: 1266   OA
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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2016 | Journal Article | IST-REx-ID: 1242   OA
Extending the dynamic range of transcription factor action by translational regulation
T.R. Sokolowski, A. Walczak, W. Bialek, G. Tkacik, Physical Review E Statistical Nonlinear and Soft Matter Physics 93 (2016).
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2016 | Journal Article | IST-REx-ID: 1420   OA
A general approximation for the dynamics of quantitative traits
K. Bod’ová, G. Tkacik, N.H. Barton, Genetics 202 (2016) 1523–1548.
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2015 | Journal Article | IST-REx-ID: 1539   OA
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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2015 | Journal Article | IST-REx-ID: 1666   OA
Dynamics of transcription factor binding site evolution
M. Tugrul, T. Paixao, N.H. Barton, G. Tkacik, PLoS Genetics 11 (2015).
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2015 | Journal Article | IST-REx-ID: 1697   OA
High accuracy decoding of dynamical motion from a large retinal population
O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkacik, M. Berry, PLoS Computational Biology 11 (2015).
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2015 | Journal Article | IST-REx-ID: 1940   OA
Optimizing information flow in small genetic networks. IV. Spatial coupling
T.R. Sokolowski, G. Tkacik, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).
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2015 | Journal Article | IST-REx-ID: 1655   OA
Quantifying emergent behavior of autonomous robots
G.S. Martius, E. Olbrich, Entropy 17 (2015) 7266–7297.
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2015 | Journal Article | IST-REx-ID: 1701   OA
Thermodynamics and signatures of criticality in a network of neurons
G. Tkacik, T. Mora, O. Marre, D. Amodei, S. Palmer, M. Berry Ii, W. Bialek, PNAS 112 (2015) 11508–11513.
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2015 | Journal Article | IST-REx-ID: 1827   OA
Evolution of bow-tie architectures in biology
T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11 (2015).
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2015 | Journal Article | IST-REx-ID: 1570   OA
Novel plasticity rule can explain the development of sensorimotor intelligence
R. Der, G.S. Martius, PNAS 112 (2015) E6224–E6232.
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2015 | Journal Article | IST-REx-ID: 1861
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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2015 | Journal Article | IST-REx-ID: 1885   OA
Positional information, positional error, and readout precision in morphogenesis: A mathematical framework
G. Tkacik, J. Dubuis, M. Petkova, T. Gregor, Genetics 199 (2015) 39–59.
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2015 | Journal Article | IST-REx-ID: 1564   OA
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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2015 | Journal Article | IST-REx-ID: 1538   OA
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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2015 | Conference Paper | IST-REx-ID: 1658
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.
View | Files available | DOI
 
2015 | Journal Article | IST-REx-ID: 1576
Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation
S.A. Cepeda Humerez, G. Rieckh, G. Tkacik, Physical Review Letters 115 (2015).
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2014 | Journal Article | IST-REx-ID: 3263   OA
Adaptation to changes in higher-order stimulus statistics in the salamander retina
G. Tkacik, A. Ghosh, E. Schneidman, R. Segev, PLoS One 9 (2014).
View | Files available | DOI
 
2014 | Journal Article | IST-REx-ID: 1896   OA
Mathematical model of alternative mechanism of telomere length maintenance
R. Kollár, K. Bod’ová, J. Nosek, Ľ. Tomáška, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).
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2014 | Journal Article | IST-REx-ID: 1928
Evolutionary dynamics of infectious diseases in finite populations
J. Humplik, A. Hill, M. Nowak, Journal of Theoretical Biology 360 (2014) 149–162.
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2014 | Journal Article | IST-REx-ID: 1909   OA
The fitness costs of adaptation via phenotypic plasticity and maternal effects
T. Ezard, R. Prizak, R. Hoyle, Functional Ecology 28 (2014) 693–701.
View | Files available | DOI
 
2014 | Journal Article | IST-REx-ID: 2231   OA
Noise and information transmission in promoters with multiple internal states
G. Rieckh, G. Tkacik, Biophysical Journal 106 (2014) 1194–1204.
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2014 | Journal Article | IST-REx-ID: 537   OA
Fitness consequences of maternal and grandmaternal effects
R. Prizak, T. Ezard, R. Hoyle, Ecology and Evolution 4 (2014) 3139–3145.
View | Files available | DOI
 
2014 | Conference Paper | IST-REx-ID: 1708
Spatio-temporal representations of uncertainty in spiking neural networks
C. Savin, S. Denève, in:, Neural Information Processing Systems, 2014, pp. 2024–2032.
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2014 | Journal Article | IST-REx-ID: 1931   OA
Emergence of task-dependent representations in working memory circuits
C. Savin, J. Triesch, Frontiers in Computational Neuroscience 8 (2014).
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2014 | Journal Article | IST-REx-ID: 1886   OA
Variance predicts salience in central sensory processing
A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, G. Tkacik, ELife (2014).
View | Files available | DOI
 
2014 | Journal Article | IST-REx-ID: 2257
Searching for collective behavior in a large network of sensory neurons
G. Tkacik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, M. Berry, PLoS Computational Biology 10 (2014).
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2013 | Journal Article | IST-REx-ID: 2277   OA
Transformation of stimulus correlations by the retina
K. Simmons, J. Prentice, G. Tkacik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, PLoS Computational Biology 9 (2013) e1003344.
View | Files available | DOI
 
2013 | Journal Article | IST-REx-ID: 2861
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) 125101.
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2013 | Book Chapter | IST-REx-ID: 2413
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.
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2013 | Journal Article | IST-REx-ID: 2913   OA
Retinal metric: a stimulus distance measure derived from population neural responses
G. Tkacik, E. Granot Atedgi, R. Segev, E. Schneidman, Physical Review Letters 110 (2013).
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2013 | Journal Article | IST-REx-ID: 2850   OA
The simplest maximum entropy model for collective behavior in a neural network
G. Tkacik, O. Marre, T. Mora, D. Amodei, M. Berry, W. Bialek, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).
View | DOI | Download (ext.) | arXiv
 
2013 | Journal Article | IST-REx-ID: 2863   OA
Stimulus-dependent maximum entropy models of neural population codes
E. Granot Atedgi, G. Tkacik, R. Segev, E. Schneidman, PLoS Computational Biology 9 (2013).
View | Files available | DOI
 
2013 | Journal Article | IST-REx-ID: 2914   OA
Statistical thermodynamics of natural images
G. Stephens, T. Mora, G. Tkacik, W. Bialek, Physical Review Letters 110 (2013) 018701.
View | Files available | DOI | Download (ext.) | arXiv
 
2013 | Journal Article | IST-REx-ID: 2851
A simple method for estimating the entropy of neural activity
M. Berry, G. Tkacik, J. Dubuis, O. Marre, R. Da Silveira, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).
View | DOI
 
2013 | Journal Article | IST-REx-ID: 2818   OA
Learning quadratic receptive fields from neural responses to natural stimuli
K. Rajan, O. Marre, G. Tkacik, Neural Computation 25 (2013) 1661–1692.
View | DOI | Download (ext.) | arXiv
 
2013 | Journal Article | IST-REx-ID: 3261   OA
Positional information, in bits
J. Dubuis, G. Tkacik, E. Wieschaus, T. Gregor, W. Bialek, PNAS 110 (2013) 16301–16308.
View | Files available | DOI | PubMed | Europe PMC
 
2013 | Journal Article | IST-REx-ID: 499
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.
View | DOI
 
2012 | Journal Article | IST-REx-ID: 3262   OA
Optimizing information flow in small genetic networks. III. A self-interacting gene
G. Tkacik, A. Walczak, W. Bialek, Physical Review E Statistical Nonlinear and Soft Matter Physics 85 (2012).
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2012 | Journal Article | IST-REx-ID: 3274
A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil
G. Rieckh, W. Kreuzer, H. Waubke, P. Balazs, Engineering Analysis with Boundary Elements 36 (2012) 960–967.
View | DOI
 
2011 | Journal Article | IST-REx-ID: 3384   OA
Natural images from the birthplace of the human eye
G. Tkacik, P. Garrigan, C. Ratliff, G. Milcinski, J. Klein, L. Seyfarth, P. Sterling, D. Brainard, V. Balasubramanian, PLoS One 6 (2011).
View | Files available | DOI
 
2011 | Journal Article | IST-REx-ID: 3374   OA
Information transmission in genetic regulatory networks a review
G. Tkacik, A. Walczak, Journal of Physics: Condensed Matter 23 (2011).
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