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.
LibreCat: https://research-explorer.ista.ac.at/record/14656
DOI: 10.1523/JNEUROSCI.0194-23.2023
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.
LibreCat: https://research-explorer.ista.ac.at/record/12487
DOI: 10.1016/j.isci.2023.107840
WoS: 001082331200001
PMID: 37766992

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.
LibreCat: https://research-explorer.ista.ac.at/record/14862
DOI: 10.1093/eurpub/ckad160.597

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
DOI: 10.1016/j.celrep.2023.113162
WoS: 001086695500001
PMID: 37777965

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).
LibreCat: https://research-explorer.ista.ac.at/record/10821
DOI: 10.1101/2022.03.03.482657

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
DOI: 10.1103/PhysRevResearch.4.023240
arXiv: 2106.02349

Eukaryotic gene regulation at equilibrium, or non?
B. Zoller, T. Gregor, G. Tkadik, Current Opinion in Systems Biology 31 (2022).
LibreCat: https://research-explorer.ista.ac.at/record/12156
DOI: 10.1016/j.coisb.2022.100435

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.
LibreCat: https://research-explorer.ista.ac.at/record/10530
DOI: 10.1016/j.bpj.2021.12.006
WoS: 000740815400007

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).
LibreCat: https://research-explorer.ista.ac.at/record/10736
DOI: 10.7554/eLife.64543
WoS: 000751104400001
PMID: 35080492

Efficient coding theory of dynamic attentional modulation
W.F. Mlynarski, G. Tkadik, PLoS Biology 20 (2022) e3001889.
LibreCat: https://research-explorer.ista.ac.at/record/12332
DOI: 10.1371/journal.pbio.3001889
WoS: 000925192000001

Accumulation and maintenance of information in evolution
M. Hledik, N.H. Barton, G. Tkadik, Proceedings of the National Academy of Sciences 119 (2022).
LibreCat: https://research-explorer.ista.ac.at/record/12081
DOI: 10.1073/pnas.2123152119
WoS: 000889278400014
PMID: 36037343

Dynamic maximum entropy provides accurate approximation of structured population dynamics
K. Bodova, E. Szep, N.H. Barton, PLoS Computational Biology 17 (2021).
LibreCat: https://research-explorer.ista.ac.at/record/10535
DOI: 10.1371/journal.pcbi.1009661
PMID: 34851948
arXiv: 2102.03669

Quantifying the coexistence of neuronal oscillations and avalanches
F. Lombardi, S. Pepic, O. Shriki, G. Tkadik, D. De Martino, (n.d.).
LibreCat: https://research-explorer.ista.ac.at/record/10912
DOI: 10.48550/ARXIV.2108.06686
arXiv: 2108.06686

Token-driven totally asymmetric simple exclusion process
B. Kavcic, G. Tkadik, ArXiv (n.d.).
LibreCat: https://research-explorer.ista.ac.at/record/10579
DOI: 10.48550/arXiv.2112.13558
arXiv: 2112.13558

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.
LibreCat: https://research-explorer.ista.ac.at/record/7463
DOI: 10.1016/j.neucom.2020.05.126
WoS: 000704086300015

The many bits of positional information
G. Tkadik, T. Gregor, Development 148 (2021).
LibreCat: https://research-explorer.ista.ac.at/record/9226
DOI: 10.1242/dev.176065
WoS: 000613906000007
PMID: 33526425

Efficient and adaptive sensory codes
W.F. Mlynarski, A.M. Hermundstad, Nature Neuroscience 24 (2021) 998–1009.
LibreCat: https://research-explorer.ista.ac.at/record/9439
DOI: 10.1038/s41593-021-00846-0
WoS: 000652577300003

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.
LibreCat: https://research-explorer.ista.ac.at/record/9822
DOI: 10.1021/acsami.1c09850
WoS: 000683741400026
PMID: 34283577

Fast and accurate amplitude demodulation of wideband signals
M. Gabrielaitis, IEEE Transactions on Signal Processing 69 (2021) 4039–4054.
LibreCat: https://research-explorer.ista.ac.at/record/9828
DOI: 10.1109/TSP.2021.3087899
WoS: 000682123900002
arXiv: 2102.04832

Inferring the function performed by a recurrent neural network
M.J. Chalk, G. Tkadik, O. Marre, PLoS ONE 16 (2021).
LibreCat: https://research-explorer.ista.ac.at/record/9362
DOI: 10.1371/journal.pone.0248940
WoS: 000641474900072
PMID: 33857170

Minimal biophysical model of combined antibiotic action
B. Kavcic, G. Tkadik, M.T. Bollenbach, PLOS Computational Biology 17 (2021).
LibreCat: https://research-explorer.ista.ac.at/record/8997
DOI: 10.1371/journal.pcbi.1008529
WoS: 000608045000010

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).
LibreCat: https://research-explorer.ista.ac.at/record/9283
DOI: 10.7554/elife.65993
WoS: 000631050900001

Statistical analysis and optimality of neural systems
W.F. Mlynarski, M. Hledik, T.R. Sokolowski, G. Tkadik, Neuron 109 (2021) 1227–1241.e5.
LibreCat: https://research-explorer.ista.ac.at/record/7553
DOI: 10.1016/j.neuron.2021.01.020
WoS: 000637809600006

The structure of hippocampal C interactions optimizes spatial coding across experience
M. Nardin, J.L. Csicsvari, G. Tkadik, C. Savin, BioRxiv (n.d.).
LibreCat: https://research-explorer.ista.ac.at/record/10077
DOI: 10.1101/2021.09.28.460602

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
DOI: 10.1051/epjconf/202023000005

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).
LibreCat: https://research-explorer.ista.ac.at/record/7490
DOI: 10.7554/eLife.52067
WoS: 000514104100001
PMID: 31971511

Distribution of crosstalk values
R. Grah, T. Friedlander, (2020).
LibreCat: https://research-explorer.ista.ac.at/record/9779
DOI: 10.1371/journal.pcbi.1007642.s003

Supporting information
R. Grah, T. Friedlander, (2020).
LibreCat: https://research-explorer.ista.ac.at/record/9776
DOI: 10.1371/journal.pcbi.1007642.s001

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

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.
LibreCat: https://research-explorer.ista.ac.at/record/8698
DOI: 10.1073/pnas.1912804117
WoS: 000579045200012
PMID: 32948691

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).
LibreCat: https://research-explorer.ista.ac.at/record/8955
DOI: 10.3389/fphys.2020.558070
WoS: 000596849400001
PMID: 33324233

Nonequilibrium models of optimal enhancer function
R. Grah, B. Zoller, G. Tkadik, PNAS 117 (2020) 31614–31622.
LibreCat: https://research-explorer.ista.ac.at/record/9000
DOI: 10.1073/pnas.2006731117
WoS: 000600608300015
PMID: 33268497

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.
LibreCat: https://research-explorer.ista.ac.at/record/8084
DOI: 10.1523/jneurosci.1278-19.2019
WoS: 000505167600016
PMID: 31694962

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.
LibreCat: https://research-explorer.ista.ac.at/record/8155
DOI: 10.15479/AT:ISTA:8155

Normative models of enhancer function
R. Grah, B. Zoller, G. Tkadik, BioRxiv (2020).
LibreCat: https://research-explorer.ista.ac.at/record/7675
DOI: 10.1101/2020.04.08.029405

The relation between crosstalk and gene regulation form revisited
R. Grah, T. Friedlander, PLOS Computational Biology 16 (2020).
LibreCat: https://research-explorer.ista.ac.at/record/7569
DOI: 10.1371/journal.pcbi.1007642
WoS: 000526725200019

Maximizing crosstalk
R. Grah, T. Friedlander, (2020).
LibreCat: https://research-explorer.ista.ac.at/record/9777
DOI: 10.1371/journal.pcbi.1007642.s002

Analysis scripts and research data for the paper "Mechanisms of drug interactions between translation-inhibiting antibiotics"
B. Kavcic, (2020).
LibreCat: https://research-explorer.ista.ac.at/record/8097
DOI: 10.15479/AT:ISTA:8097

Analysis scripts and research data for the paper "Minimal biophysical model of combined antibiotic action"
B. Kavcic, (2020).
LibreCat: https://research-explorer.ista.ac.at/record/8930
DOI: 10.15479/AT:ISTA:8930

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

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.
LibreCat: https://research-explorer.ista.ac.at/record/8657
DOI: 10.15479/AT:ISTA:8657

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

A minimal biophysical model of combined antibiotic action
B. Kavcic, G. Tkadik, M.T. Bollenbach, BioRxiv (2020).
LibreCat: https://research-explorer.ista.ac.at/record/7673
DOI: 10.1101/2020.04.18.047886

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.
LibreCat: https://research-explorer.ista.ac.at/record/7652
DOI: 10.1038/s41559-020-1132-7
WoS: 000519008300005

Action at a distance in transcriptional regulation
W. Bialek, T. Gregor, G. Tkadik, ArXiv:1912.08579 (n.d.).
LibreCat: https://research-explorer.ista.ac.at/record/7552
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.
LibreCat: https://research-explorer.ista.ac.at/record/5945
DOI: 10.1016/j.cell.2019.01.007
WoS: 000457969200015
PMID: 30712870

Feedback-induced self-oscillations in large interacting systems subjected to phase transitions
D. De Martino, Journal of Physics A: Mathematical and Theoretical 52 (2019).
LibreCat: https://research-explorer.ista.ac.at/record/6049
DOI: 10.1088/1751-8121/aaf2dd
WoS: 000455379500001

Temporal order and precision of complex stress responses in individual bacteria
K. Mitosch, G. Rieckh, M.T. Bollenbach, Molecular Systems Biology 15 (2019).
LibreCat: https://research-explorer.ista.ac.at/record/6046
DOI: 10.15252/msb.20188470
WoS: 000459628300003
PMID: 30765425

Molecular noise of innate immunity shapes bacteria-phage ecologies
J. Ruess, M. Pleska, C.C. Guet, G. Tkadik, PLoS Computational Biology 15 (2019).
LibreCat: https://research-explorer.ista.ac.at/record/6784
DOI: 10.1371/journal.pcbi.1007168
WoS: 000481577700032

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