M. Narasimhan et al., “Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants,” eLife, vol. 9. eLife Sciences Publications, 2020.
LibreCat: https://research-explorer.ista.ac.at/record/7490
DOI: 10.7554/eLife.52067
WoS: 000514104100001
PMID: 31971511

R. Grah and T. Friedlander, “Distribution of crosstalk values.” Public Library of Science, 2020.
LibreCat: https://research-explorer.ista.ac.at/record/9779
DOI: 10.1371/journal.pcbi.1007642.s003

R. Grah and T. Friedlander, “Supporting information.” Public Library of Science, 2020.
LibreCat: https://research-explorer.ista.ac.at/record/9776
DOI: 10.1371/journal.pcbi.1007642.s001

M. J. Berry and G. Tkadik, “Clustering of neural activity: A design principle for population codes,” Frontiers in Computational Neuroscience, vol. 14. Frontiers, 2020.
LibreCat: https://research-explorer.ista.ac.at/record/7656
DOI: 10.3389/fncom.2020.00020
WoS: 000525543200001
PMID: 32231528

O. Maoz, G. Tkadik, M. S. Esteki, R. Kiani, and E. Schneidman, “Learning probabilistic neural representations with randomly connected circuits,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40. National Academy of Sciences, pp. 25066–25073, 2020.
LibreCat: https://research-explorer.ista.ac.at/record/8698
DOI: 10.1073/pnas.1912804117
WoS: 000579045200012
PMID: 32948691

R. Rizzo, X. Zhang, J. W. J. L. Wang, F. Lombardi, and P. C. Ivanov, “Network physiology of cortico–muscular interactions,” Frontiers in Physiology, vol. 11. Frontiers, 2020.
LibreCat: https://research-explorer.ista.ac.at/record/8955
DOI: 10.3389/fphys.2020.558070
WoS: 000596849400001
PMID: 33324233

R. Grah, B. Zoller, and G. Tkadik, “Nonequilibrium models of optimal enhancer function,” PNAS, vol. 117, no. 50. National Academy of Sciences, pp. 31614–31622, 2020.
LibreCat: https://research-explorer.ista.ac.at/record/9000
DOI: 10.1073/pnas.2006731117
WoS: 000600608300015
PMID: 33268497

F. Lombardi et al., “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,” Journal of Neuroscience, vol. 40, no. 1. Society for Neuroscience, pp. 171–190, 2020.
LibreCat: https://research-explorer.ista.ac.at/record/8084
DOI: 10.1523/jneurosci.1278-19.2019
WoS: 000505167600016
PMID: 31694962

R. Grah, “Gene regulation across scales – how biophysical constraints shape evolution,” Institute of Science and Technology Austria, 2020.
LibreCat: https://research-explorer.ista.ac.at/record/8155
DOI: 10.15479/AT:ISTA:8155

R. Grah, B. Zoller, and G. Tkadik, “Normative models of enhancer function,” bioRxiv. Cold Spring Harbor Laboratory, 2020.
LibreCat: https://research-explorer.ista.ac.at/record/7675
DOI: 10.1101/2020.04.08.029405

R. Grah and T. Friedlander, “The relation between crosstalk and gene regulation form revisited,” PLOS Computational Biology, vol. 16, no. 2. Public Library of Science, 2020.
LibreCat: https://research-explorer.ista.ac.at/record/7569
DOI: 10.1371/journal.pcbi.1007642
WoS: 000526725200019

R. Grah and T. Friedlander, “Maximizing crosstalk.” Public Library of Science, 2020.
LibreCat: https://research-explorer.ista.ac.at/record/9777
DOI: 10.1371/journal.pcbi.1007642.s002

B. Kavcic, “Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics.’” Institute of Science and Technology Austria, 2020.
LibreCat: https://research-explorer.ista.ac.at/record/8097
DOI: 10.15479/AT:ISTA:8097

B. Kavcic, “Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action.’” Institute of Science and Technology Austria, 2020.
LibreCat: https://research-explorer.ista.ac.at/record/8930
DOI: 10.15479/AT:ISTA:8930

R. Grah, “Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation.” Institute of Science and Technology Austria, 2020.
LibreCat: https://research-explorer.ista.ac.at/record/7383
DOI: 10.15479/AT:ISTA:7383

B. Kavcic, “Perturbations of protein synthesis: from antibiotics to genetics and physiology,” Institute of Science and Technology Austria, 2020.
LibreCat: https://research-explorer.ista.ac.at/record/8657
DOI: 10.15479/AT:ISTA:8657

B. Kavcic, G. Tkadik, and M. T. Bollenbach, “Mechanisms of drug interactions between translation-inhibiting antibiotics,” Nature Communications, vol. 11. Springer Nature, 2020.
LibreCat: https://research-explorer.ista.ac.at/record/8250
DOI: 10.1038/s41467-020-17734-z
WoS: 000562769300008

B. Kavcic, G. Tkadik, and M. T. Bollenbach, “A minimal biophysical model of combined antibiotic action,” bioRxiv. Cold Spring Harbor Laboratory, 2020.
LibreCat: https://research-explorer.ista.ac.at/record/7673
DOI: 10.1101/2020.04.18.047886

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

S. Deny, O. Marre, V. Botella-Soler, G. S. Martius, and G. Tkadik, “Nonlinear decoding of a complex movie from the mammalian retina.” Institute of Science and Technology Austria, 2018.
LibreCat: https://research-explorer.ista.ac.at/record/5584
DOI: 10.15479/AT:ISTA:98

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

D. De Martino and G. Tkadik, “Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018.
LibreCat: https://research-explorer.ista.ac.at/record/5587
DOI: 10.15479/AT:ISTA:62