Tipping points of space debris in low earth orbit
K. Nomura, S. Rella, H. Merritt, M. Baltussen, D. Bird, A. Tjuka, D. Falk, International Journal of the Commons 18 (2024).
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Genetic information and biological optimization
M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024.
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Dynamic pathogen detection and social feedback shape collective hygiene in ants
B.E. Casillas Perez, K. Bodova, A.V. Grasse, G. Tkadik, S. Cremer, Nature Communications 14 (2023).
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Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain
F. Lombardi, S. Pepic, O. Shriki, G. Tkadik, D. De Martino, Nature Computational Science 3 (2023) 254–263.
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arXiv: 2108.06686

Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories
M. Reinhardt, G. Tkadik, P.R. Ten Wolde, Physical Review X 13 (2023).
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arXiv: 2203.03461

The structure of hippocampal C interactions optimizes spatial coding across experience
M. Nardin, J.L. Csicsvari, G. Tkadik, C. Savin, The Journal of Neuroscience 43 (2023) 8140–8156.
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PMID: 37758476

Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture
S. Scarpetta, N. Morrisi, C. Mutti, N. Azzi, I. Trippi, R. Ciliento, I. Apicella, G. Messuti, M. Angiolelli, F. Lombardi, L. Parrino, A.E. Vaudano, IScience 26 (2023) 107840.
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Complex vaccination strategies prevent the emergence of vaccine resistance
S. Rella, Y. Kulikova, A. Minnegalieva, F. Kondrashov, in:, European Journal of Public Health, Oxford University Press, 2023.
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Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state
F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano, L. De Arcangelis, O. Shriki, Cell Reports 42 (2023).
LibreCat: https://research-explorer.ista.ac.at/record/14402
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Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades
F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano, L. de Arcangelis, O. Shriki, BioRxiv (2022).
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Inferring couplings in networks across order-disorder phase transitions
V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D.J. Schwab, S.E. Palmer, Physical Review Research 4 (2022).
LibreCat: https://research-explorer.ista.ac.at/record/11638
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arXiv: 2106.02349

Eukaryotic gene regulation at equilibrium, or non?
B. Zoller, T. Gregor, G. Tkadik, Current Opinion in Systems Biology 31 (2022).
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Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration
T. Zisis, D. Brückner, T. Brandstätter, W.X. Siow, J. d’Alessandro, A.M. Vollmar, C.P. Broedersz, S. Zahler, Biophysical Journal 121 (2022) -60.
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Predicting bacterial promoter function and evolution from random sequences
M. Lagator, S. Sarikas, M. Steinrueck, D. Toledo-Aparicio, J.P. Bollback, C.C. Guet, G. Tkadik, ELife 11 (2022).
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Efficient coding theory of dynamic attentional modulation
W.F. Mlynarski, G. Tkadik, PLoS Biology 20 (2022) e3001889.
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Accumulation and maintenance of information in evolution
M. Hledik, N.H. Barton, G. Tkadik, Proceedings of the National Academy of Sciences 119 (2022).
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Dynamic maximum entropy provides accurate approximation of structured population dynamics
K. Bodova, E. Szep, N.H. Barton, PLoS Computational Biology 17 (2021).
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Quantifying the coexistence of neuronal oscillations and avalanches
F. Lombardi, S. Pepic, O. Shriki, G. Tkadik, D. De Martino, (n.d.).
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Token-driven totally asymmetric simple exclusion process
B. Kavcic, G. Tkadik, ArXiv (n.d.).
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Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches
F. Lombardi, O. Shriki, H.J. Herrmann, L. de Arcangelis, Neurocomputing 461 (2021) 657–666.
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The many bits of positional information
G. Tkadik, T. Gregor, Development 148 (2021).
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Efficient and adaptive sensory codes
W.F. Mlynarski, A.M. Hermundstad, Nature Neuroscience 24 (2021) 998–1009.
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Sequential and switchable patterning for studying cellular processes under spatiotemporal control
T. Zisis, J. Schwarz, M. Balles, M. Kretschmer, M. Nemethova, R.P. Chait, R. Hauschild, J. Lange, C.C. Guet, M.K. Sixt, S. Zahler, ACS Applied Materials and Interfaces 13 (2021) 35545–35560.
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Fast and accurate amplitude demodulation of wideband signals
M. Gabrielaitis, IEEE Transactions on Signal Processing 69 (2021) 4039–4054.
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Inferring the function performed by a recurrent neural network
M.J. Chalk, G. Tkadik, O. Marre, PLoS ONE 16 (2021).
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Minimal biophysical model of combined antibiotic action
B. Kavcic, G. Tkadik, M.T. Bollenbach, PLOS Computational Biology 17 (2021).
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Local genetic context shapes the function of a gene regulatory network
A.A. Nagy-Staron, K. Tomasek, C. Caruso Carter, E. Sonnleitner, B. Kavcic, T. Paixão, C.C. Guet, ELife 10 (2021).
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Statistical analysis and optimality of neural systems
W.F. Mlynarski, M. Hledik, T.R. Sokolowski, G. Tkadik, Neuron 109 (2021) 1227–1241.e5.
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The structure of hippocampal C interactions optimizes spatial coding across experience
M. Nardin, J.L. Csicsvari, G. Tkadik, C. Savin, BioRxiv (n.d.).
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Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality
F. Lombardi, J.W.J.L. Wang, X. Zhang, P.C. Ivanov, EPJ Web of Conferences 230 (2020).
LibreCat: https://research-explorer.ista.ac.at/record/8105
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Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants
M. Narasimhan, A.J. Johnson, R. Prizak, W. Kaufmann, S. Tan, B.E. Casillas Perez, J. Friml, ELife 9 (2020).
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Clustering of neural activity: A design principle for population codes
M.J. Berry, G. Tkadik, Frontiers in Computational Neuroscience 14 (2020).
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Learning probabilistic neural representations with randomly connected circuits
O. Maoz, G. Tkadik, M.S. Esteki, R. Kiani, E. Schneidman, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 25066–25073.
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Network physiology of cortico–muscular interactions
R. Rizzo, X. Zhang, J.W.J.L. Wang, F. Lombardi, P.C. Ivanov, Frontiers in Physiology 11 (2020).
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Nonequilibrium models of optimal enhancer function
R. Grah, B. Zoller, G. Tkadik, PNAS 117 (2020) 31614–31622.
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Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake
F. Lombardi, M. Gómez-Extremera, P. Bernaola-Galván, R. Vetrivelan, C.B. Saper, T.E. Scammell, P.C. Ivanov, Journal of Neuroscience 40 (2020) 171–190.
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Gene regulation across scales – how biophysical constraints shape evolution
R. Grah, Gene Regulation across Scales – How Biophysical Constraints Shape Evolution, Institute of Science and Technology Austria, 2020.
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Normative models of enhancer function
R. Grah, B. Zoller, G. Tkadik, BioRxiv (2020).
LibreCat: https://research-explorer.ista.ac.at/record/7675
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The relation between crosstalk and gene regulation form revisited
R. Grah, T. Friedlander, PLOS Computational Biology 16 (2020).
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Perturbations of protein synthesis: from antibiotics to genetics and physiology
B. Kavcic, Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology, Institute of Science and Technology Austria, 2020.
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Mechanisms of drug interactions between translation-inhibiting antibiotics
B. Kavcic, G. Tkadik, M.T. Bollenbach, Nature Communications 11 (2020).
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A minimal biophysical model of combined antibiotic action
B. Kavcic, G. Tkadik, M.T. Bollenbach, BioRxiv (2020).
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Gene amplification as a form of population-level gene expression regulation
I. Tomanek, R. Grah, M. Lagator, A.M.C. Andersson, J.P. Bollback, G. Tkadik, C.C. Guet, Nature Ecology &; Evolution 4 (2020) 612–625.
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Action at a distance in transcriptional regulation
W. Bialek, T. Gregor, G. Tkadik, ArXiv:1912.08579 (n.d.).
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arXiv: 1912.08579

Optimal decoding of cellular identities in a genetic network
M.D. Petkova, G. Tkadik, W. Bialek, E.F. Wieschaus, T. Gregor, Cell 176 (2019) 844–855.e15.
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Feedback-induced self-oscillations in large interacting systems subjected to phase transitions
D. De Martino, Journal of Physics A: Mathematical and Theoretical 52 (2019).
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Temporal order and precision of complex stress responses in individual bacteria
K. Mitosch, G. Rieckh, M.T. Bollenbach, Molecular Systems Biology 15 (2019).
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Molecular noise of innate immunity shapes bacteria-phage ecologies
J. Ruess, M. Pleska, C.C. Guet, G. Tkadik, PLoS Computational Biology 15 (2019).
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eGFRD in all dimensions
T.R. Sokolowski, J. Paijmans, L. Bossen, T. Miedema, M. Wehrens, N.B. Becker, K. Kaizu, K. Takahashi, M. Dogterom, P.R. ten Wolde, The Journal of Chemical Physics 150 (2019).
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Estimating information in time-varying signals
S.A. Cepeda Humerez, J. Ruess, G. Tkadik, PLoS Computational Biology 15 (2019) e1007290.
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Harmonic dynamics of the Abelian sandpile
M. Lang, M. Shkolnikov, Proceedings of the National Academy of Sciences 116 (2019) 2821–2830.
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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).
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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.
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An introduction to the maximum entropy approach and its application to inference problems in biology
A. De Martino, D. De Martino, Heliyon 4 (2018).
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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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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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Probabilistic models of individual and collective animal behavior
K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkadik, PLoS One 13 (2018).
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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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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).
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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.
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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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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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WoS: 000400985000001
arXiv: 1410.1242

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).
LibreCat: https://research-explorer.ista.ac.at/record/1104
DOI: 10.1038/s41467-017-02159-y
WoS: 000417241200004

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

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

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
DOI: 10.1103/PhysRevE.95.062419
WoS: 000404546400004

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).
LibreCat: https://research-explorer.ista.ac.at/record/947
DOI: 10.1103/PhysRevE.96.010401
WoS: 000405194200002

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.
LibreCat: https://research-explorer.ista.ac.at/record/943
DOI: 10.1126/science.aam5887
WoS: 000404351500036
PMID: 28663499

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

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

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

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

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.
LibreCat: https://research-explorer.ista.ac.at/record/665
DOI: 10.1126/science.aaf4762

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