Hledik M, Sokolowski TR, Tkadik G. 2019. A tight upper bound on mutual information. IEEE Information Theory Workshop, ITW 2019. Information Theory Workshop, 8989292.
LibreCat: https://research-explorer.ista.ac.at/record/7606
DOI: 10.1109/ITW44776.2019.8989292
WoS: 000540384500015
arXiv: 1812.01475

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

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

Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkadik G, Swain P. 2018. Distributed and dynamic intracellular organization of extracellular information. PNAS. 115(23), 6088–6093.
LibreCat: https://research-explorer.ista.ac.at/record/281
DOI: 10.1073/pnas.1716659115
WoS: 000434114900071
PMID: 29784812

Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 209(3), 861–883.
LibreCat: https://research-explorer.ista.ac.at/record/316
DOI: 10.1534/genetics.118.300748
WoS: 000437171700017

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

Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkadik G. 2018. Probabilistic models of individual and collective animal behavior. PLoS One. 13(3).
LibreCat: https://research-explorer.ista.ac.at/record/406
DOI: 10.1371/journal.pone.0193049
WoS: 000426896800032

Pleska M, Lang M, Refardt D, Levin B, Guet CC. 2018. Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. 2(2), 359–366.
LibreCat: https://research-explorer.ista.ac.at/record/457
DOI: 10.1038/s41559-017-0424-z
WoS: 000426516400027

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

Ferrari U, Deny S, Chalk MJ, Tkadik G, Marre O, Mora T. 2018. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 98(4), 042410.
LibreCat: https://research-explorer.ista.ac.at/record/31
DOI: 10.1103/PhysRevE.98.042410
WoS: 000447486100004

Chalk MJ, Marre O, Tkadik G. 2018. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 115(1), 186–191.
LibreCat: https://research-explorer.ista.ac.at/record/543
DOI: 10.1073/pnas.1711114115
WoS: 000419128700049

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

Palmer A, Chait RP, Kishony R. 2018. Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. 35(11), 2669–2684.
LibreCat: https://research-explorer.ista.ac.at/record/19
DOI: 10.1093/molbev/msy163
WoS: 000452567200006
PMID: 30169679

Botella Soler V, Deny S, Martius GS, Marre O, Tkadik G. 2018. Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology. 14(5), e1006057.
LibreCat: https://research-explorer.ista.ac.at/record/292
DOI: 10.1371/journal.pcbi.1006057
WoS: 000434012100002

De Martino D, Mc AA, Bergmiller T, Guet CC, Tkadik G. 2018. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 9(1), 2988.
LibreCat: https://research-explorer.ista.ac.at/record/161
DOI: 10.1038/s41467-018-05417-9
WoS: 000440149300021

Igler C, Lagator M, Tkadik G, Bollback JP, Guet CC. 2018. Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. 2(10), 1633–1643.
LibreCat: https://research-explorer.ista.ac.at/record/67
DOI: 10.1038/s41559-018-0651-y
WoS: 000447947600021

Chait RP, Ruess J, Bergmiller T, Tkadik G, Guet CC. 2017. Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. 8(1), 1535.
LibreCat: https://research-explorer.ista.ac.at/record/613
DOI: 10.1038/s41467-017-01683-1

Der R, Martius GS. 2017. Dynamical self consistency leads to behavioral development and emergent social interactions in robots. ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics , 7846789.
LibreCat: https://research-explorer.ista.ac.at/record/652
DOI: 10.1109/DEVLRN.2016.7846789

Der R, Martius GS. 2017. Self organized behavior generation for musculoskeletal robots. Frontiers in Neurorobotics. 11(MAR), 00008.
LibreCat: https://research-explorer.ista.ac.at/record/658
DOI: 10.3389/fnbot.2017.00008

Humplik J, Tkadik G. 2017. Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. 13(9), e1005763.
LibreCat: https://research-explorer.ista.ac.at/record/720
DOI: 10.1371/journal.pcbi.1005763

Harpaz R, Tkadik G, Schneidman E. 2017. Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. 114(38), 10149–10154.
LibreCat: https://research-explorer.ista.ac.at/record/725
DOI: 10.1073/pnas.1703817114
PMID: 28874581

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

Chalk MJ, Masset P, Gutkin B, Denève S. 2017. Sensory noise predicts divisive reshaping of receptive fields. PLoS Computational Biology. 13(6), e1005582.
LibreCat: https://research-explorer.ista.ac.at/record/680
DOI: 10.1371/journal.pcbi.1005582

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

Mitosch K, Rieckh G, Bollenbach MT. 2017. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. 4(4), 393–403.
LibreCat: https://research-explorer.ista.ac.at/record/666
DOI: 10.1016/j.cels.2017.03.001

Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. 2017. Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of Statistics. 44(2), 285–306.
LibreCat: https://research-explorer.ista.ac.at/record/2016
DOI: 10.1111/sjos.12251
WoS: 000400985000001
arXiv: 1410.1242

Deny S, Ferrari U, Mace E, Yger P, Caplette R, Picaud S, Tkadik G, Marre O. 2017. Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. 8(1), 1964.
LibreCat: https://research-explorer.ista.ac.at/record/1104
DOI: 10.1038/s41467-017-02159-y
WoS: 000417241200004

Levina (Martius) A, Priesemann V. 2017. Subsampling scaling. Nature Communications. 8, 15140.
LibreCat: https://research-explorer.ista.ac.at/record/993
DOI: 10.1038/ncomms15140
WoS: 000400560700001

Friedlander T, Prizak R, Barton NH, Tkadik G. 2017. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 8(1), 216.
LibreCat: https://research-explorer.ista.ac.at/record/955
DOI: 10.1038/s41467-017-00238-8
WoS: 000407198800005

De Martino D. 2017. Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics.  Physical Review E Statistical Nonlinear and Soft Matter Physics . 95(6), 062419.
LibreCat: https://research-explorer.ista.ac.at/record/959
DOI: 10.1103/PhysRevE.95.062419
WoS: 000404546400004

De Martino D, Capuani F, De Martino A. 2017. Quantifying the entropic cost of cellular growth control.  Physical Review E Statistical Nonlinear and Soft Matter Physics . 96(1), 010401.
LibreCat: https://research-explorer.ista.ac.at/record/947
DOI: 10.1103/PhysRevE.96.010401
WoS: 000405194200002

Zagórski MP, Tabata Y, Brandenberg N, Lutolf M, Tkadik G, Bollenbach T, Briscoe J, Kicheva A. 2017. Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. 356(6345), 1379–1383.
LibreCat: https://research-explorer.ista.ac.at/record/943
DOI: 10.1126/science.aam5887
WoS: 000404351500036
PMID: 28663499

Colabrese S, De Martino D, Leuzzi L, Marinari E. 2017. Phase transitions in integer linear problems.  Journal of Statistical Mechanics: Theory and Experiment. 2017(9), 093404.
LibreCat: https://research-explorer.ista.ac.at/record/823
DOI: 10.1088/1742-5468/aa85c3
WoS: 000411842900001

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

De Martino D. 2017. Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. Physical Review E. 96(6), 060401.
LibreCat: https://research-explorer.ista.ac.at/record/548
DOI: 10.1103/PhysRevE.96.060401

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

Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkadik G, Guet CC. 2017. Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science. 356(6335), 311–315.
LibreCat: https://research-explorer.ista.ac.at/record/665
DOI: 10.1126/science.aaf4762

Barone V, Lang M, Krens G, Pradhan S, Shamipour S, Sako K, Sikora MK, Guet CC, Heisenberg C-PJ. 2017. An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. Developmental Cell. 43(2), 198–211.
LibreCat: https://research-explorer.ista.ac.at/record/735
DOI: 10.1016/j.devcel.2017.09.014
WoS: 000413443700011

Chalk MJ, Marre O, Tkadik G. 2016. Relevant sparse codes with variational information bottleneck. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 1965–1973.
LibreCat: https://research-explorer.ista.ac.at/record/1082

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

Lang M, Stelling J. 2016. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 38(6), 8–08.
LibreCat: https://research-explorer.ista.ac.at/record/1170
DOI: 10.1137/15M103306X

Tkadik G. 2016. 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. 17, 166–167.
LibreCat: https://research-explorer.ista.ac.at/record/1171
DOI: 10.1016/j.plrev.2016.06.005

De Martino D, Masoero D. 2016. Asymptotic analysis of noisy fitness maximization, applied to metabolism &;amp; growth.  Journal of Statistical Mechanics: Theory and Experiment. 2016(12), 123502.
LibreCat: https://research-explorer.ista.ac.at/record/1188
DOI: 10.1088/1742-5468/aa4e8f

Hu F, Rishishwar L, Sivadas A, Mitchell G, King J, Murphy T, Gilsdorf J, Mayer L, Wang X. 2016. Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. Journal of Clinical Microbiology. 54(12), 3010–3017.
LibreCat: https://research-explorer.ista.ac.at/record/1203
DOI: 10.1128/JCM.01511-16

Martius GS, Hostettler R, Knoll A, Der R. 2016. Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm. IEEE RSJ International Conference on Intelligent Robots and Systems IROS  vol. 2016–November, 7759138.
LibreCat: https://research-explorer.ista.ac.at/record/1214
DOI: 10.1109/IROS.2016.7759138

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

Sokolowski TR, Walczak A, Bialek W, Tkadik G. 2016. Extending the dynamic range of transcription factor action by translational regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. 93(2), 022404.
LibreCat: https://research-explorer.ista.ac.at/record/1242
DOI: 10.1103/PhysRevE.93.022404

Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. 2016. Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. PNAS. 113(7), 1811–1816.
LibreCat: https://research-explorer.ista.ac.at/record/1244
DOI: 10.1073/pnas.1419248113

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

De Martino D. 2016. The dual of the space of interactions in neural network models. International Journal of Modern Physics C. 27(6), 1650067.
LibreCat: https://research-explorer.ista.ac.at/record/1260
DOI: 10.1142/S0129183116500674
arXiv: 1505.02963