Please note that LibreCat no longer supports Internet Explorer versions 8 or 9 (or earlier).
We recommend upgrading to the latest Internet Explorer, Google Chrome, or Firefox.
174 Publications
2023 | Journal Article | IST-REx-ID: 14656 | 
Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” The Journal of Neuroscience. Society of Neuroscience, 2023. https://doi.org/10.1523/JNEUROSCI.0194-23.2023.
[Published Version]
View
| Files available
| DOI
| Download Published Version (ext.)
| PubMed | Europe PMC
2023 | Journal Article | IST-REx-ID: 12487 |
Scarpetta, Silvia, Niccolò Morrisi, Carlotta Mutti, Nicoletta Azzi, Irene Trippi, Rosario Ciliento, Ilenia Apicella, et al. “Criticality of Neuronal Avalanches in Human Sleep and Their Relationship with Sleep Macro- and Micro-Architecture.” IScience. Elsevier, 2023. https://doi.org/10.1016/j.isci.2023.107840.
[Published Version]
View
| Files available
| DOI
| WoS
| PubMed | Europe PMC
2023 | Conference Abstract | IST-REx-ID: 14862 |
Rella, Simon, Y Kulikova, Aygul Minnegalieva, and Fyodor Kondrashov. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” In European Journal of Public Health, Vol. 33. Oxford University Press, 2023. https://doi.org/10.1093/eurpub/ckad160.597.
[Published Version]
View
| Files available
| DOI
2023 | Journal Article | IST-REx-ID: 14402 |
Lombardi, Fabrizio, Hans J. Herrmann, Liborio Parrino, Dietmar Plenz, Silvia Scarpetta, Anna Elisabetta Vaudano, Lucilla De Arcangelis, and Oren Shriki. “Beyond Pulsed Inhibition: Alpha Oscillations Modulate Attenuation and Amplification of Neural Activity in the Awake Resting State.” Cell Reports. Elsevier, 2023. https://doi.org/10.1016/j.celrep.2023.113162.
[Published Version]
View
| Files available
| DOI
| WoS
| PubMed | Europe PMC
2022 | Preprint | IST-REx-ID: 10821 |
Lombardi, Fabrizio, Hans J. Herrmann, Liborio Parrino, Dietmar Plenz, Silvia Scarpetta, Anna Elisabetta Vaudano, Lucilla de Arcangelis, and Oren Shriki. “Alpha Rhythm Induces Attenuation-Amplification Dynamics in Neural Activity Cascades.” BioRxiv. Cold Spring Harbor Laboratory, 2022. https://doi.org/10.1101/2022.03.03.482657.
[Preprint]
View
| DOI
| Download Preprint (ext.)
2022 | Journal Article | IST-REx-ID: 11638 |
Ngampruetikorn, Vudtiwat, Vedant Sachdeva, Johanna Torrence, Jan Humplik, David J. Schwab, and Stephanie E. Palmer. “Inferring Couplings in Networks across Order-Disorder Phase Transitions.” Physical Review Research. American Physical Society, 2022. https://doi.org/10.1103/PhysRevResearch.4.023240.
[Published Version]
View
| Files available
| DOI
| arXiv
2022 | Journal Article | IST-REx-ID: 12156 |
Zoller, Benjamin, Thomas Gregor, and Gašper Tkačik. “Eukaryotic Gene Regulation at Equilibrium, or Non?” Current Opinion in Systems Biology. Elsevier, 2022. https://doi.org/10.1016/j.coisb.2022.100435.
[Published Version]
View
| Files available
| DOI
2022 | Journal Article | IST-REx-ID: 10530 |
Zisis, Themistoklis, David Brückner, Tom Brandstätter, Wei Xiong Siow, Joseph d’Alessandro, Angelika M. Vollmar, Chase P. Broedersz, and Stefan Zahler. “Disentangling Cadherin-Mediated Cell-Cell Interactions in Collective Cancer Cell Migration.” Biophysical Journal. Elsevier, 2022. https://doi.org/10.1016/j.bpj.2021.12.006.
[Published Version]
View
| Files available
| DOI
| WoS
2022 | Journal Article | IST-REx-ID: 10736 |
Lagator, Mato, Srdjan Sarikas, Magdalena Steinrueck, David Toledo-Aparicio, Jonathan P Bollback, Calin C Guet, and Gašper Tkačik. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” ELife. eLife Sciences Publications, 2022. https://doi.org/10.7554/eLife.64543.
[Published Version]
View
| Files available
| DOI
| WoS
| PubMed | Europe PMC
2022 | Journal Article | IST-REx-ID: 12332 |
Mlynarski, Wiktor F, and Gašper Tkačik. “Efficient Coding Theory of Dynamic Attentional Modulation.” PLoS Biology. Public Library of Science, 2022. https://doi.org/10.1371/journal.pbio.3001889.
[Published Version]
View
| Files available
| DOI
| WoS
2022 | Journal Article | IST-REx-ID: 12081 |
Hledik, Michal, Nicholas H Barton, and Gašper Tkačik. “Accumulation and Maintenance of Information in Evolution.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2123152119.
[Published Version]
View
| Files available
| DOI
| WoS
| PubMed | Europe PMC
2021 | Journal Article | IST-REx-ID: 10535 |
Bodova, Katarina, Eniko Szep, and Nicholas H Barton. “Dynamic Maximum Entropy Provides Accurate Approximation of Structured Population Dynamics.” PLoS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1009661.
[Published Version]
View
| Files available
| DOI
| PubMed | Europe PMC
| arXiv
2021 | Preprint | IST-REx-ID: 10912 |
Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele De Martino. “Quantifying the Coexistence of Neuronal Oscillations and Avalanches.” arXiv, n.d. https://doi.org/10.48550/ARXIV.2108.06686.
[Preprint]
View
| DOI
| Download Preprint (ext.)
| arXiv
2021 | Preprint | IST-REx-ID: 10579 |
Kavcic, Bor, and Gašper Tkačik. “Token-Driven Totally Asymmetric Simple Exclusion Process.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2112.13558.
[Preprint]
View
| DOI
| Download Preprint (ext.)
| arXiv
2021 | Journal Article | IST-REx-ID: 7463 |
Lombardi, Fabrizio, Oren Shriki, Hans J Herrmann, and Lucilla de Arcangelis. “Long-Range Temporal Correlations in the Broadband Resting State Activity of the Human Brain Revealed by Neuronal Avalanches.” Neurocomputing. Elsevier, 2021. https://doi.org/10.1016/j.neucom.2020.05.126.
[Preprint]
View
| DOI
| Download Preprint (ext.)
| WoS
2021 | Journal Article | IST-REx-ID: 9226 |
Tkačik, Gašper, and Thomas Gregor. “The Many Bits of Positional Information.” Development. The Company of Biologists, 2021. https://doi.org/10.1242/dev.176065.
[Published Version]
View
| DOI
| Download Published Version (ext.)
| WoS
| PubMed | Europe PMC
2021 | Journal Article | IST-REx-ID: 9439 |
Mlynarski, Wiktor F, and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.” Nature Neuroscience. Springer Nature, 2021. https://doi.org/10.1038/s41593-021-00846-0.
[Preprint]
View
| DOI
| Download Preprint (ext.)
| WoS
2021 | Journal Article | IST-REx-ID: 9822 |
Zisis, Themistoklis, Jan Schwarz, Miriam Balles, Maibritt Kretschmer, Maria Nemethova, Remy P Chait, Robert Hauschild, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and Interfaces. American Chemical Society, 2021. https://doi.org/10.1021/acsami.1c09850.
[Published Version]
View
| Files available
| DOI
| WoS
| PubMed | Europe PMC
2021 | Journal Article | IST-REx-ID: 9828 |
Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband Signals.” IEEE Transactions on Signal Processing. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/TSP.2021.3087899.
[Preprint]
View
| DOI
| Download Preprint (ext.)
| WoS
| arXiv
2021 | Journal Article | IST-REx-ID: 9362 |
Chalk, Matthew J, Gašper Tkačik, and Olivier Marre. “Inferring the Function Performed by a Recurrent Neural Network.” PLoS ONE. Public Library of Science, 2021. https://doi.org/10.1371/journal.pone.0248940.
[Published Version]
View
| Files available
| DOI
| WoS
| PubMed | Europe PMC
2021 | Journal Article | IST-REx-ID: 8997 |
Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Minimal Biophysical Model of Combined Antibiotic Action.” PLOS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1008529.
[Published Version]
View
| Files available
| DOI
| WoS
2021 | Journal Article | IST-REx-ID: 9283 |
Nagy-Staron, Anna A, Kathrin Tomasek, Caroline Caruso Carter, Elisabeth Sonnleitner, Bor Kavcic, Tiago Paixão, and Calin C Guet. “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.65993.
[Published Version]
View
| Files available
| DOI
| WoS
2021 | Journal Article | IST-REx-ID: 7553 |
Mlynarski, Wiktor F, Michal Hledik, Thomas R Sokolowski, and Gašper Tkačik. “Statistical Analysis and Optimality of Neural Systems.” Neuron. Cell Press, 2021. https://doi.org/10.1016/j.neuron.2021.01.020.
[Preprint]
View
| Files available
| DOI
| Download Preprint (ext.)
| WoS
2021 | Preprint | IST-REx-ID: 10077 |
Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2021.09.28.460602.
[Preprint]
View
| Files available
| DOI
| Download Preprint (ext.)
2020 | Journal Article | IST-REx-ID: 8105 |
Lombardi, Fabrizio, Jilin W.J.L. Wang, Xiyun Zhang, and Plamen Ch Ivanov. “Power-Law Correlations and Coupling of Active and Quiet States Underlie a Class of Complex Systems with Self-Organization at Criticality.” EPJ Web of Conferences. EDP Sciences, 2020. https://doi.org/10.1051/epjconf/202023000005.
[Published Version]
View
| Files available
| DOI
2020 | Journal Article | IST-REx-ID: 7490 |
Narasimhan, Madhumitha, Alexander J Johnson, Roshan Prizak, Walter Kaufmann, Shutang Tan, Barbara E Casillas Perez, and Jiří Friml. “Evolutionarily Unique Mechanistic Framework of Clathrin-Mediated Endocytosis in Plants.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.52067.
[Published Version]
View
| Files available
| DOI
| WoS
| PubMed | Europe PMC
2020 | Research Data Reference | IST-REx-ID: 9779
Grah, Rok, and Tamar Friedlander. “Distribution of Crosstalk Values.” Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s003.
[Published Version]
View
| Files available
| DOI
2020 | Research Data Reference | IST-REx-ID: 9776
Grah, Rok, and Tamar Friedlander. “Supporting Information.” Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s001.
[Published Version]
View
| Files available
| DOI
2020 | Journal Article | IST-REx-ID: 7656 |
Berry, Michael J., and Gašper Tkačik. “Clustering of Neural Activity: A Design Principle for Population Codes.” Frontiers in Computational Neuroscience. Frontiers, 2020. https://doi.org/10.3389/fncom.2020.00020.
[Published Version]
View
| Files available
| DOI
| WoS
| PubMed | Europe PMC
2020 | Journal Article | IST-REx-ID: 8698 |
Maoz, Ori, Gašper Tkačik, Mohamad Saleh Esteki, Roozbeh Kiani, and Elad Schneidman. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1912804117.
[Published Version]
View
| Files available
| DOI
| WoS
| PubMed | Europe PMC
2020 | Journal Article | IST-REx-ID: 8955 |
Rizzo, Rossella, Xiyun Zhang, Jilin W.J.L. Wang, Fabrizio Lombardi, and Plamen Ch Ivanov. “Network Physiology of Cortico–Muscular Interactions.” Frontiers in Physiology. Frontiers, 2020. https://doi.org/10.3389/fphys.2020.558070.
[Published Version]
View
| Files available
| DOI
| WoS
| PubMed | Europe PMC
2020 | Journal Article | IST-REx-ID: 9000 |
Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Nonequilibrium Models of Optimal Enhancer Function.” PNAS. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2006731117.
[Published Version]
View
| Files available
| DOI
| WoS
| PubMed | Europe PMC
2020 | Journal Article | IST-REx-ID: 8084 |
Lombardi, Fabrizio, Manuel Gómez-Extremera, Pedro Bernaola-Galván, Ramalingam Vetrivelan, Clifford B. Saper, Thomas E. Scammell, and Plamen Ch. Ivanov. “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. Society for Neuroscience, 2020. https://doi.org/10.1523/jneurosci.1278-19.2019.
[Published Version]
View
| Files available
| DOI
| WoS
| PubMed | Europe PMC
2020 | Thesis | IST-REx-ID: 8155 |
Grah, Rok. “Gene Regulation across Scales – How Biophysical Constraints Shape Evolution.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8155.
[Published Version]
View
| Files available
| DOI
2020 | Preprint | IST-REx-ID: 7675 |
Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Normative Models of Enhancer Function.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.04.08.029405.
[Preprint]
View
| Files available
| DOI
| Download Preprint (ext.)
2020 | Journal Article | IST-REx-ID: 7569 |
Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.” PLOS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.
[Published Version]
View
| Files available
| DOI
| WoS
2020 | Research Data Reference | IST-REx-ID: 9777 |
Grah, Rok, and Tamar Friedlander. “Maximizing Crosstalk.” Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s002.
View
| Files available
| DOI
| Download None (ext.)
2020 | Thesis | IST-REx-ID: 8657 |
Kavcic, Bor. “Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8657.
[Published Version]
View
| Files available
| DOI
2020 | Journal Article | IST-REx-ID: 8250 |
Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17734-z.
[Published Version]
View
| Files available
| DOI
| WoS
2020 | Preprint | IST-REx-ID: 7673 |
Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “A Minimal Biophysical Model of Combined Antibiotic Action.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.04.18.047886.
[Preprint]
View
| Files available
| DOI
| Download Preprint (ext.)
2020 | Journal Article | IST-REx-ID: 7652 |
Tomanek, Isabella, Rok Grah, M. Lagator, A. M. C. Andersson, Jonathan P Bollback, Gašper Tkačik, and Calin C Guet. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Nature Ecology & Evolution. Springer Nature, 2020. https://doi.org/10.1038/s41559-020-1132-7.
[Submitted Version]
View
| Files available
| DOI
| WoS
2019 | Preprint | IST-REx-ID: 7552 |
Bialek, William, Thomas Gregor, and Gašper Tkačik. “Action at a Distance in Transcriptional Regulation.” ArXiv:1912.08579. ArXiv, n.d.
[Preprint]
View
| Download Preprint (ext.)
| arXiv
2019 | Journal Article | IST-REx-ID: 5945 |
Petkova, Mariela D., Gašper Tkačik, William Bialek, Eric F. Wieschaus, and Thomas Gregor. “Optimal Decoding of Cellular Identities in a Genetic Network.” Cell. Cell Press, 2019. https://doi.org/10.1016/j.cell.2019.01.007.
[Published Version]
View
| Files available
| DOI
| Download Published Version (ext.)
| WoS
| PubMed | Europe PMC
2019 | Journal Article | IST-REx-ID: 6049 |
De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting Systems Subjected to Phase Transitions.” Journal of Physics A: Mathematical and Theoretical. IOP Publishing, 2019. https://doi.org/10.1088/1751-8121/aaf2dd.
[Published Version]
View
| Files available
| DOI
| WoS
2019 | Journal Article | IST-REx-ID: 6046 |
Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Temporal Order and Precision of Complex Stress Responses in Individual Bacteria.” Molecular Systems Biology. Embo Press, 2019. https://doi.org/10.15252/msb.20188470.
[Submitted Version]
View
| DOI
| Download Submitted Version (ext.)
| WoS
| PubMed | Europe PMC
2019 | Journal Article | IST-REx-ID: 6784 |
Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” PLoS Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007168.
[Published Version]
View
| Files available
| DOI
| WoS
2019 | Research Data Reference | IST-REx-ID: 9786
Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Supporting Text and Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007168.s001.
[Published Version]
View
| Files available
| DOI
2019 | Journal Article | IST-REx-ID: 7422 |
Sokolowski, Thomas R, Joris Paijmans, Laurens Bossen, Thomas Miedema, Martijn Wehrens, Nils B. Becker, Kazunari Kaizu, Koichi Takahashi, Marileen Dogterom, and Pieter Rein ten Wolde. “EGFRD in All Dimensions.” The Journal of Chemical Physics. AIP Publishing, 2019. https://doi.org/10.1063/1.5064867.
[Preprint]
View
| DOI
| Download Preprint (ext.)
| WoS
| arXiv
2019 | Journal Article | IST-REx-ID: 6900 |
Cepeda Humerez, Sarah A, Jakob Ruess, and Gašper Tkačik. “Estimating Information in Time-Varying Signals.” PLoS Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007290.
[Published Version]
View
| Files available
| DOI
| WoS
| PubMed | Europe PMC
2019 | Journal Article | IST-REx-ID: 196 |
Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian Sandpile.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1812015116.
[Published Version]
View
| Files available
| DOI
| Download Published Version (ext.)
| WoS
| PubMed | Europe PMC
| arXiv