I. Tomanek et al., “Gene amplification as a form of population-level gene expression regulation,” Nature Ecology &; Evolution, vol. 4, no. 4. Springer Nature, pp. 612–625, 2020.
LibreCat: https://research-explorer.ista.ac.at/record/7652
DOI: 10.1038/s41559-020-1132-7
WoS: 000519008300005

W. Bialek, T. Gregor, and G. Tkadik, “Action at a distance in transcriptional regulation,” arXiv:1912.08579. ArXiv.
LibreCat: https://research-explorer.ista.ac.at/record/7552
arXiv: 1912.08579

M. D. Petkova, G. Tkadik, W. Bialek, E. F. Wieschaus, and T. Gregor, “Optimal decoding of cellular identities in a genetic network,” Cell, vol. 176, no. 4. Cell Press, p. 844–855.e15, 2019.
LibreCat: https://research-explorer.ista.ac.at/record/5945
DOI: 10.1016/j.cell.2019.01.007
WoS: 000457969200015
PMID: 30712870

D. De Martino, “Feedback-induced self-oscillations in large interacting systems subjected to phase transitions,” Journal of Physics A: Mathematical and Theoretical, vol. 52, no. 4. IOP Publishing, 2019.
LibreCat: https://research-explorer.ista.ac.at/record/6049
DOI: 10.1088/1751-8121/aaf2dd
WoS: 000455379500001

K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Temporal order and precision of complex stress responses in individual bacteria,” Molecular systems biology, vol. 15, no. 2. Embo Press, 2019.
LibreCat: https://research-explorer.ista.ac.at/record/6046
DOI: 10.15252/msb.20188470
WoS: 000459628300003
PMID: 30765425

J. Ruess, M. Pleska, C. C. Guet, and G. Tkadik, “Molecular noise of innate immunity shapes bacteria-phage ecologies,” PLoS Computational Biology, vol. 15, no. 7. Public Library of Science, 2019.
LibreCat: https://research-explorer.ista.ac.at/record/6784
DOI: 10.1371/journal.pcbi.1007168
WoS: 000481577700032

J. Ruess, M. Pleska, C. C. Guet, and G. Tkadik, “Supporting text and results.” Public Library of Science, 2019.
LibreCat: https://research-explorer.ista.ac.at/record/9786
DOI: 10.1371/journal.pcbi.1007168.s001

T. R. Sokolowski et al., GFRD in all dimensions,” The Journal of Chemical Physics, vol. 150, no. 5. AIP Publishing, 2019.
LibreCat: https://research-explorer.ista.ac.at/record/7422
DOI: 10.1063/1.5064867
WoS: 000458109300009
arXiv: 1708.09364

S. A. Cepeda Humerez, J. Ruess, and G. Tkadik, “Estimating information in time-varying signals,” PLoS computational biology, vol. 15, no. 9. Public Library of Science, p. e1007290, 2019.
LibreCat: https://research-explorer.ista.ac.at/record/6900
DOI: 10.1371/journal.pcbi.1007290
WoS: 000489741800021
PMID: 31479447

M. Lang and M. Shkolnikov, “Harmonic dynamics of the Abelian sandpile,” Proceedings of the National Academy of Sciences, vol. 116, no. 8. National Academy of Sciences, pp. 2821–2830, 2019.
LibreCat: https://research-explorer.ista.ac.at/record/196
DOI: 10.1073/pnas.1812015116
WoS: 000459074400013
PMID:  30728300
arXiv: 1806.10823

B. Kavcic, A. Sakashita, H. Noguchi, and P. Ziherl, “Limiting shapes of confined lipid vesicles,” Soft Matter, vol. 15, no. 4. Royal Society of Chemistry, pp. 602–614, 2019.
LibreCat: https://research-explorer.ista.ac.at/record/5817
DOI: 10.1039/c8sm01956h
WoS: 000457329700003
PMID: 30629082

S. A. Cepeda Humerez, “Estimating information flow in single cells,” Institute of Science and Technology Austria, 2019.
LibreCat: https://research-explorer.ista.ac.at/record/6473
DOI: 10.15479/AT:ISTA:6473

R. Prizak, “Coevolution of transcription factors and their binding sites in sequence space,” Institute of Science and Technology Austria, 2019.
LibreCat: https://research-explorer.ista.ac.at/record/6071
DOI: 10.15479/at:ista:th6071

J. W. J. L. Wang, F. Lombardi, X. Zhang, C. Anaclet, and P. C. Ivanov, “Non-equilibrium critical dynamics of bursts in ;8 and ;4 rhythms as fundamental characteristic of sleep and wake micro-architecture,” PLoS Computational Biology, vol. 15, no. 11. Public Library of Science, 2019.
LibreCat: https://research-explorer.ista.ac.at/record/7103
DOI: 10.1371/journal.pcbi.1007268
WoS: 000500976100014
PMID: 31725712

M. Carballo-Pacheco et al., “Receptor crosstalk improves concentration sensing of multiple ligands,” Physical Review E, vol. 99, no. 2. American Physical Society, 2019.
LibreCat: https://research-explorer.ista.ac.at/record/6090
DOI: 10.1103/PhysRevE.99.022423
WoS: 000459916500007

M. Hledik, T. R. Sokolowski, and G. Tkadik, “A tight upper bound on mutual information,” in IEEE Information Theory Workshop, ITW 2019, Visby, Sweden, 2019.
LibreCat: https://research-explorer.ista.ac.at/record/7606
DOI: 10.1109/ITW44776.2019.8989292
WoS: 000540384500015
arXiv: 1812.01475

A. De Martino and D. De Martino, “An introduction to the maximum entropy approach and its application to inference problems in biology,” Heliyon, vol. 4, no. 4. Elsevier, 2018.
LibreCat: https://research-explorer.ista.ac.at/record/306
DOI: 10.1016/j.heliyon.2018.e00596

P. Misun, A. Birchler, M. Lang, A. Hierlemann, and O. Frey, “Fabrication and operation of microfluidic hanging drop networks,” Methods in Molecular Biology, vol. 1771. Springer, pp. 183–202, 2018.
LibreCat: https://research-explorer.ista.ac.at/record/305
DOI: 10.1007/978-1-4939-7792-5_15

A. Granados, J. Pietsch, S. A. Cepeda Humerez, I. Farquhar, G. Tkadik, and P. Swain, “Distributed and dynamic intracellular organization of extracellular information,” PNAS, vol. 115, no. 23. National Academy of Sciences, pp. 6088–6093, 2018.
LibreCat: https://research-explorer.ista.ac.at/record/281
DOI: 10.1073/pnas.1716659115
WoS: 000434114900071
PMID: 29784812

K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system,” Genetics, vol. 209, no. 3. Genetics Society of America, pp. 861–883, 2018.
LibreCat: https://research-explorer.ista.ac.at/record/316
DOI: 10.1534/genetics.118.300748
WoS: 000437171700017

K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Supplemental material for Bodova et al., 2018.” Genetics Society of America, 2018.
LibreCat: https://research-explorer.ista.ac.at/record/9813
DOI: 10.25386/genetics.6148304.v1

K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkadik, “Probabilistic models of individual and collective animal behavior,” PLoS One, vol. 13, no. 3. Public Library of Science, 2018.
LibreCat: https://research-explorer.ista.ac.at/record/406
DOI: 10.1371/journal.pone.0193049
WoS: 000426896800032

M. Pleska, M. Lang, D. Refardt, B. Levin, and C. C. Guet, “Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity,” Nature Ecology and Evolution, vol. 2, no. 2. Springer Nature, pp. 359–366, 2018.
LibreCat: https://research-explorer.ista.ac.at/record/457
DOI: 10.1038/s41559-017-0424-z
WoS: 000426516400027

K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkadik, “Implementation of the inference method in Matlab.” Public Library of Science, 2018.
LibreCat: https://research-explorer.ista.ac.at/record/9831
DOI: 10.1371/journal.pone.0193049.s001

U. Ferrari, S. Deny, M. J. Chalk, G. Tkadik, O. Marre, and T. Mora, “Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons,” Physical Review E, vol. 98, no. 4. American Physical Society, 2018.
LibreCat: https://research-explorer.ista.ac.at/record/31
DOI: 10.1103/PhysRevE.98.042410
WoS: 000447486100004

M. J. Chalk, O. Marre, and G. Tkadik, “Toward a unified theory of efficient, predictive, and sparse coding,” PNAS, vol. 115, no. 1. National Academy of Sciences, pp. 186–191, 2018.
LibreCat: https://research-explorer.ista.ac.at/record/543
DOI: 10.1073/pnas.1711114115
WoS: 000419128700049

K. Bodova, J. Haskovec, and P. Markowich, “Well posedness and maximum entropy approximation for the dynamics of quantitative traits,” Physica D: Nonlinear Phenomena, vol. 376–377. Elsevier, pp. 108–120, 2018.
LibreCat: https://research-explorer.ista.ac.at/record/607
DOI: 10.1016/j.physd.2017.10.015
WoS: 000437962900012
arXiv: 1704.08757

A. Palmer, R. P. Chait, and R. Kishony, “Nonoptimal gene expression creates latent potential for antibiotic resistance,” Molecular Biology and Evolution, vol. 35, no. 11. Oxford University Press, pp. 2669–2684, 2018.
LibreCat: https://research-explorer.ista.ac.at/record/19
DOI: 10.1093/molbev/msy163
WoS: 000452567200006
PMID: 30169679

V. Botella Soler, S. Deny, G. S. Martius, O. Marre, and G. Tkadik, “Nonlinear decoding of a complex movie from the mammalian retina,” PLoS Computational Biology, vol. 14, no. 5. Public Library of Science, 2018.
LibreCat: https://research-explorer.ista.ac.at/record/292
DOI: 10.1371/journal.pcbi.1006057
WoS: 000434012100002

D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkadik, “Statistical mechanics for metabolic networks during steady state growth,” Nature Communications, vol. 9, no. 1. Springer Nature, 2018.
LibreCat: https://research-explorer.ista.ac.at/record/161
DOI: 10.1038/s41467-018-05417-9
WoS: 000440149300021

C. Igler, M. Lagator, G. Tkadik, J. P. Bollback, and C. C. Guet, “Evolutionary potential of transcription factors for gene regulatory rewiring,” Nature Ecology and Evolution, vol. 2, no. 10. Nature Publishing Group, pp. 1633–1643, 2018.
LibreCat: https://research-explorer.ista.ac.at/record/67
DOI: 10.1038/s41559-018-0651-y
WoS: 000447947600021

R. P. Chait, J. Ruess, T. Bergmiller, G. Tkadik, and C. C. Guet, “Shaping bacterial population behavior through computer interfaced control of individual cells,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/613
DOI: 10.1038/s41467-017-01683-1

R. Der and G. S. Martius, “Dynamical self consistency leads to behavioral development and emergent social interactions in robots,” presented at the ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics , Cergy-Pontoise, France, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/652
DOI: 10.1109/DEVLRN.2016.7846789

R. Der and G. S. Martius, “Self organized behavior generation for musculoskeletal robots,” Frontiers in Neurorobotics, vol. 11, no. MAR. Frontiers Research Foundation, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/658
DOI: 10.3389/fnbot.2017.00008

J. Humplik and G. Tkadik, “Probabilistic models for neural populations that naturally capture global coupling and criticality,” PLoS Computational Biology, vol. 13, no. 9. Public Library of Science, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/720
DOI: 10.1371/journal.pcbi.1005763

R. Harpaz, G. Tkadik, and E. Schneidman, “Discrete modes of social information processing predict individual behavior of fish in a group,” PNAS, vol. 114, no. 38. National Academy of Sciences, pp. 10149–10154, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/725
DOI: 10.1073/pnas.1703817114
PMID: 28874581

J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkadik, and M. Berry, “Data from: Error-robust modes of the retinal population code.” Dryad, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/9709
DOI: 10.5061/dryad.1f1rc

M. J. Chalk, P. Masset, B. Gutkin, and S. Denève, “Sensory noise predicts divisive reshaping of receptive fields,” PLoS Computational Biology, vol. 13, no. 6. Public Library of Science, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/680
DOI: 10.1371/journal.pcbi.1005582

M. J. Chalk, P. Masset, B. Gutkin, and S. Denève, “Supplementary appendix.” Public Library of Science, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/9855
DOI: 10.1371/journal.pcbi.1005582.s001

K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment,” Cell Systems, vol. 4, no. 4. Cell Press, pp. 393–403, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/666
DOI: 10.1016/j.cels.2017.03.001

A. Martin Del Campo Sanchez, S. A. Cepeda Humerez, and C. Uhler, “Exact goodness-of-fit testing for the Ising model,” Scandinavian Journal of Statistics, vol. 44, no. 2. Wiley-Blackwell, pp. 285–306, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/2016
DOI: 10.1111/sjos.12251
WoS: 000400985000001
arXiv: 1410.1242

S. Deny et al., “Multiplexed computations in retinal ganglion cells of a single type,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/1104
DOI: 10.1038/s41467-017-02159-y
WoS: 000417241200004

A. Levina (Martius) and V. Priesemann, “Subsampling scaling,” Nature Communications, vol. 8. Nature Publishing Group, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/993
DOI: 10.1038/ncomms15140
WoS: 000400560700001

T. Friedlander, R. Prizak, N. H. Barton, and G. Tkadik, “Evolution of new regulatory functions on biophysically realistic fitness landscapes,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/955
DOI: 10.1038/s41467-017-00238-8
WoS: 000407198800005

D. De Martino, “Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics,”  Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 95, no. 6. American Institute of Physics, p. 062419, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/959
DOI: 10.1103/PhysRevE.95.062419
WoS: 000404546400004

D. De Martino, F. Capuani, and A. De Martino, “Quantifying the entropic cost of cellular growth control,”  Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1. American Institute of Physics, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/947
DOI: 10.1103/PhysRevE.96.010401
WoS: 000405194200002

M. P. Zagórski et al., “Decoding of position in the developing neural tube from antiparallel morphogen gradients,” Science, vol. 356, no. 6345. American Association for the Advancement of Science, pp. 1379–1383, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/943
DOI: 10.1126/science.aam5887
WoS: 000404351500036
PMID: 28663499

S. Colabrese, D. De Martino, L. Leuzzi, and E. Marinari, “Phase transitions in integer linear problems,”  Journal of Statistical Mechanics: Theory and Experiment, vol. 2017, no. 9. IOPscience, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/823
DOI: 10.1088/1742-5468/aa85c3
WoS: 000411842900001

C. Savin and G. Tkadik, “Maximum entropy models as a tool for building precise neural controls,” Current Opinion in Neurobiology, vol. 46. Elsevier, pp. 120–126, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/730
DOI: 10.1016/j.conb.2017.08.001
WoS: 000416196400016

D. De Martino, “Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes,” Physical Review E, vol. 96, no. 6. American Physical Society, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/548
DOI: 10.1103/PhysRevE.96.060401

M. Lang and E. Sontag, “Zeros of nonlinear systems with input invariances,” Automatica, vol. 81C. International Federation of Automatic Control, pp. 46–55, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/1007
DOI: 10.1016/j.automatica.2017.03.030
WoS: 000403513900006

T. Bergmiller et al., “Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity,” Science, vol. 356, no. 6335. American Association for the Advancement of Science, pp. 311–315, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/665
DOI: 10.1126/science.aaf4762

V. Barone et al., “An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate,” Developmental Cell, vol. 43, no. 2. Cell Press, pp. 198–211, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/735
DOI: 10.1016/j.devcel.2017.09.014
WoS: 000413443700011

M. J. Chalk, O. Marre, and G. Tkadik, “Relevant sparse codes with variational information bottleneck,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 1965–1973.
LibreCat: https://research-explorer.ista.ac.at/record/1082

C. Savin and G. Tkadik, “Estimating nonlinear neural response functions using GP priors and Kronecker methods,” presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain, 2016, vol. 29, pp. 3610–3618.
LibreCat: https://research-explorer.ista.ac.at/record/1105

M. Lang and J. Stelling, “Modular parameter identification of biomolecular networks,” SIAM Journal on Scientific Computing, vol. 38, no. 6. Society for Industrial and Applied Mathematics , pp. 8–08, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1170
DOI: 10.1137/15M103306X

G. Tkadik, “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.,” Physics of Life Reviews, vol. 17. Elsevier, pp. 166–167, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1171
DOI: 10.1016/j.plrev.2016.06.005

D. De Martino and D. Masoero, “Asymptotic analysis of noisy fitness maximization, applied to metabolism &;amp; growth,”  Journal of Statistical Mechanics: Theory and Experiment, vol. 2016, no. 12. IOPscience, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1188
DOI: 10.1088/1742-5468/aa4e8f

F. Hu et al., “Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination,” Journal of Clinical Microbiology, vol. 54, no. 12. American Society for Microbiology, pp. 3010–3017, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1203
DOI: 10.1128/JCM.01511-16

G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm,” presented at the IEEE RSJ International Conference on Intelligent Robots and Systems IROS , Daejeon, Korea, 2016, vol. 2016–November.
LibreCat: https://research-explorer.ista.ac.at/record/1214
DOI: 10.1109/IROS.2016.7759138

G. Miki, A. Stoll, J. Bevirt, R. Grah, and M. Moore, “Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency,” presented at the AIAA: Aviation Technology, Integration, and Operations Conference, Washington, D.C., USA, 2016, pp. 1–19.
LibreCat: https://research-explorer.ista.ac.at/record/1220
DOI: 10.2514/6.2016-3764

T. R. Sokolowski, A. Walczak, W. Bialek, and G. Tkadik, “Extending the dynamic range of transcription factor action by translational regulation,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 93, no. 2. American Institute of Physics, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1242
DOI: 10.1103/PhysRevE.93.022404

P. Recouvreux, T. R. Sokolowski, A. Grammoustianou, P. Tenwolde, and M. Dogterom, “Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells,” PNAS, vol. 113, no. 7. National Academy of Sciences, pp. 1811–1816, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1244
DOI: 10.1073/pnas.1419248113

G. Tkadik and W. Bialek, “Information processing in living systems,” Annual Review of Condensed Matter Physics, vol. 7. Annual Reviews, pp. 89–117, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1248
DOI: 10.1146/annurev-conmatphys-031214-014803

D. De Martino, “The dual of the space of interactions in neural network models,” International Journal of Modern Physics C, vol. 27, no. 6. World Scientific Publishing, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1260
DOI: 10.1142/S0129183116500674
arXiv: 1505.02963

M. J. Chalk, B. Gutkin, and S. Denève, “Neural oscillations as a signature of efficient coding in the presence of synaptic delays,” eLife, vol. 5, no. 2016JULY. eLife Sciences Publications, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1266
DOI: 10.7554/eLife.13824

L. Stone, M. Baym, T. Lieberman, R. P. Chait, J. Clardy, and R. Kishony, “Compounds that select against the tetracycline-resistance efflux pump,” Nature Chemical Biology, vol. 12, no. 11. Nature Publishing Group, pp. 902–904, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1290
DOI: 10.1038/nchembio.2176

M. Lang and E. Sontag, “Scale-invariant systems realize nonlinear differential operators,” presented at the ACC: American Control Conference, Boston, MA, USA, 2016, vol. 2016–July.
LibreCat: https://research-explorer.ista.ac.at/record/1320
DOI: 10.1109/ACC.2016.7526722

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

M. Baym et al., “Spatiotemporal microbial evolution on antibiotic landscapes,” Science, vol. 353, no. 6304. American Association for the Advancement of Science, pp. 1147–1151, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1342
DOI: 10.1126/science.aag0822

D. De Martino, F. Capuani, and A. De Martino, “Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli,” Physical Biology, vol. 13, no. 3. IOP Publishing Ltd., 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1394
DOI: 10.1088/1478-3975/13/3/036005

K. Bodova, G. Tkadik, and N. H. Barton, “A general approximation for the dynamics of quantitative traits,” Genetics, vol. 202, no. 4. Genetics Society of America, pp. 1523–1548, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1420
DOI: 10.1534/genetics.115.184127
arXiv: 1510.08344

D. De Martino, “Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis,” Physical Biology, vol. 13, no. 1. IOP Publishing Ltd., 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1485
DOI: 10.1088/1478-3975/13/1/016003

C. Schilling, S. Bogomolov, T. A. Henzinger, A. Podelski, and J. Ruess, “Adaptive moment closure for parameter inference of biochemical reaction networks,” Biosystems, vol. 149. Elsevier, pp. 15–25, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1148
DOI: 10.1016/j.biosystems.2016.07.005

G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Self-organized control of an tendon driven arm by differential extrinsic plasticity,” in Proceedings of the Artificial Life Conference 2016, Cancun, Mexico, 2016, vol. 28, pp. 142–143.
LibreCat: https://research-explorer.ista.ac.at/record/8094
DOI: 10.7551/978-0-262-33936-0-ch029

J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkadik, and M. Berry, “Error-robust modes of the retinal population code,” PLoS Computational Biology, vol. 12, no. 11. Public Library of Science, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1197
DOI: 10.1371/journal.pcbi.1005148

T. Monk, C. Savin, and J. Lücke, “Neurons equipped with intrinsic plasticity learn stimulus intensity statistics,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine, 2016, vol. 29, pp. 4285–4293.
LibreCat: https://research-explorer.ista.ac.at/record/948

P. Hillenbrand, U. Gerland, and G. Tkadik, “Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information,” PLoS One, vol. 11, no. 9. Public Library of Science, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1270
DOI: 10.1371/journal.pone.0163628

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

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

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

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

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

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

J. Ruess, “Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space,” Journal of Chemical Physics, vol. 143, no. 24. American Institute of Physics, 2015.
LibreCat: https://research-explorer.ista.ac.at/record/1539
DOI: 10.1063/1.4937937

J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, and J. Lygeros, “Iterative experiment design guides the characterization of a light-inducible gene expression circuit,” PNAS, vol. 112, no. 26. National Academy of Sciences, pp. 8148–8153, 2015.
LibreCat: https://research-explorer.ista.ac.at/record/1538
DOI: 10.1073/pnas.1423947112
PMID: 26085136

M. Gilson, C. Savin, and F. Zenke, “Editorial: Emergent neural computation from the interaction of different forms of plasticity,” Frontiers in Computational Neuroscience, vol. 9, no. 11. Frontiers Research Foundation, 2015.
LibreCat: https://research-explorer.ista.ac.at/record/1564
DOI: 10.3389/fncom.2015.00145

R. Der and G. S. Martius, “Novel plasticity rule can explain the development of sensorimotor intelligence,” PNAS, vol. 112, no. 45. National Academy of Sciences, pp. 24–32, 2015.
LibreCat: https://research-explorer.ista.ac.at/record/1570
DOI: 10.1073/pnas.1508400112
PMID: 26504200

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

O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkadik, and M. Berry, “High accuracy decoding of dynamical motion from a large retinal population,” PLoS Computational Biology, vol. 11, no. 7. Public Library of Science, 2015.
LibreCat: https://research-explorer.ista.ac.at/record/1697
DOI: 10.1371/journal.pcbi.1004304

G. Tkadik et al., “Thermodynamics and signatures of criticality in a network of neurons,” PNAS, vol. 112, no. 37. National Academy of Sciences, pp. 11508–11513, 2015.
LibreCat: https://research-explorer.ista.ac.at/record/1701
DOI: 10.1073/pnas.1514188112
PMID: 26330611

J. Ruess and J. Lygeros, “Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks,” ACM Transactions on Modeling and Computer Simulation, vol. 25, no. 2. ACM, 2015.
LibreCat: https://research-explorer.ista.ac.at/record/1861
DOI: 10.1145/2688906

G. Tkadik, J. Dubuis, M. Petkova, and T. Gregor, “Positional information, positional error, and readout precision in morphogenesis: A mathematical framework,” Genetics, vol. 199, no. 1. Genetics Society of America, pp. 39–59, 2015.
LibreCat: https://research-explorer.ista.ac.at/record/1885
DOI: 10.1534/genetics.114.171850

T. R. Sokolowski and G. Tkadik, “Optimizing information flow in small genetic networks. IV. Spatial coupling,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 6. American Institute of Physics, 2015.
LibreCat: https://research-explorer.ista.ac.at/record/1940
DOI: 10.1103/PhysRevE.91.062710

T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Supporting information text.” Public Library of Science, 2015.
LibreCat: https://research-explorer.ista.ac.at/record/9718
DOI: 10.1371/journal.pcbi.1004055.s001

T. Friedlander, A. Mayo, T. Tlusty, and U. Alon, “Evolution of bow-tie architectures in biology,” PLoS Computational Biology, vol. 11, no. 3. Public Library of Science, 2015.
LibreCat: https://research-explorer.ista.ac.at/record/1827
DOI: 10.1371/journal.pcbi.1004055

T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Evolutionary simulation code.” Public Library of Science, 2015.
LibreCat: https://research-explorer.ista.ac.at/record/9773
DOI: 10.1371/journal.pcbi.1004055.s002

M. Tugrul, T. Paixao, N. H. Barton, and G. Tkadik, “Other fitness models for comparison &; for interacting TFBSs.” Public Library of Science, 2015.
LibreCat: https://research-explorer.ista.ac.at/record/9712
DOI: 10.1371/journal.pgen.1005639.s001

M. Tugrul, T. Paixao, N. H. Barton, and G. Tkadik, “Dynamics of transcription factor binding site evolution,” PLoS Genetics, vol. 11, no. 11. Public Library of Science, 2015.
LibreCat: https://research-explorer.ista.ac.at/record/1666
DOI: 10.1371/journal.pgen.1005639

S. A. Cepeda Humerez, G. Rieckh, and G. Tkadik, “Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation,” Physical Review Letters, vol. 115, no. 24. American Physical Society, 2015.
LibreCat: https://research-explorer.ista.ac.at/record/1576
DOI: 10.1103/PhysRevLett.115.248101