Nomura, Keiko, Simon Rella, Haily Merritt, Mathieu Baltussen, Darcy Bird, Annika Tjuka, and Dan Falk. “Tipping Points of Space Debris in Low Earth Orbit.”https://doi.org/10.5334/ijc.1275__International Journal of the Commons. Ubiquity Press, 2024.https://doi.org/10.5334/ijc.1275 .

Hledik, Michal. “Genetic Information and Biological Optimization.”https://doi.org/10.15479/at:ista:15020__Institute of Science and Technology Austria, 2024.https://doi.org/10.15479/at:ista:15020 .

Casillas Perez, Barbara E, Katarina Bodova, Anna V Grasse, Gasper Tkadik, and Sylvia Cremer. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.”https://doi.org/10.1038/s41467-023-38947-y__Nature Communications. Springer Nature, 2023.https://doi.org/10.1038/s41467-023-38947-y .

Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gasper Tkadik, and Daniele De Martino. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.”https://doi.org/10.1038/s43588-023-00410-9__Nature Computational Science. Springer Nature, 2023.https://doi.org/10.1038/s43588-023-00410-9 .

Reinhardt, Manuel, Gasper Tkadik, and Pieter Rein Ten Wolde. “Path Weight Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic Trajectories.”https://doi.org/10.1103/PhysRevX.13.041017__Physical Review X. American Physical Society, 2023.https://doi.org/10.1103/PhysRevX.13.041017 .

Nardin, Michele, Jozsef L Csicsvari, Gasper Tkadik, and Cristina Savin. “The Structure of Hippocampal C Interactions Optimizes Spatial Coding across Experience.”https://doi.org/10.1523/JNEUROSCI.0194-23.2023__The Journal of Neuroscience. Society of Neuroscience, 2023.https://doi.org/10.1523/JNEUROSCI.0194-23.2023 .

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.”https://doi.org/10.1016/j.isci.2023.107840__IScience. Elsevier, 2023.https://doi.org/10.1016/j.isci.2023.107840 .

Rella, Simon, Y Kulikova, Aygul Minnegalieva, and Fyodor Kondrashov. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.”https://doi.org/10.1093/eurpub/ckad160.597__In European Journal of Public Health, Vol. 33. Oxford University Press, 2023.https://doi.org/10.1093/eurpub/ckad160.597 .

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.”https://doi.org/10.1016/j.celrep.2023.113162__Cell Reports. Elsevier, 2023.https://doi.org/10.1016/j.celrep.2023.113162 .

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.”https://doi.org/10.1101/2022.03.03.482657__BioRxiv. Cold Spring Harbor Laboratory, 2022.https://doi.org/10.1101/2022.03.03.482657 .

Ngampruetikorn, Vudtiwat, Vedant Sachdeva, Johanna Torrence, Jan Humplik, David J. Schwab, and Stephanie E. Palmer. “Inferring Couplings in Networks across Order-Disorder Phase Transitions.”https://doi.org/10.1103/PhysRevResearch.4.023240__Physical Review Research. American Physical Society, 2022.https://doi.org/10.1103/PhysRevResearch.4.023240 .

Zoller, Benjamin, Thomas Gregor, and Gasper Tkadik. “Eukaryotic Gene Regulation at Equilibrium, or Non?”https://doi.org/10.1016/j.coisb.2022.100435__Current Opinion in Systems Biology. Elsevier, 2022.https://doi.org/10.1016/j.coisb.2022.100435 .

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.”https://doi.org/10.1016/j.bpj.2021.12.006__Biophysical Journal. Elsevier, 2022.https://doi.org/10.1016/j.bpj.2021.12.006 .

Lagator, Mato, Srdjan Sarikas, Magdalena Steinrueck, David Toledo-Aparicio, Jonathan P Bollback, Calin C Guet, and Gasper Tkadik. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.”https://doi.org/10.7554/eLife.64543__ELife. eLife Sciences Publications, 2022.https://doi.org/10.7554/eLife.64543 .

Mlynarski, Wiktor F, and Gasper Tkadik. “Efficient Coding Theory of Dynamic Attentional Modulation.”https://doi.org/10.1371/journal.pbio.3001889__PLoS Biology. Public Library of Science, 2022.https://doi.org/10.1371/journal.pbio.3001889 .

Hledik, Michal, Nicholas H Barton, and Gasper Tkadik. “Accumulation and Maintenance of Information in Evolution.”https://doi.org/10.1073/pnas.2123152119__Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2022.https://doi.org/10.1073/pnas.2123152119 .

Bodova, Katarina, Eniko Szep, and Nicholas H Barton. “Dynamic Maximum Entropy Provides Accurate Approximation of Structured Population Dynamics.”https://doi.org/10.1371/journal.pcbi.1009661__PLoS Computational Biology. Public Library of Science, 2021.https://doi.org/10.1371/journal.pcbi.1009661 .

Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gasper Tkadik, and Daniele De Martino. “Quantifying the Coexistence of Neuronal Oscillations and Avalanches.”https://doi.org/10.48550/ARXIV.2108.06686__arXiv, n.d.https://doi.org/10.48550/ARXIV.2108.06686 .

Kavcic, Bor, and Gasper Tkadik. “Token-Driven Totally Asymmetric Simple Exclusion Process.”https://doi.org/10.48550/arXiv.2112.13558__ArXiv, n.d.https://doi.org/10.48550/arXiv.2112.13558 .

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.”https://doi.org/10.1016/j.neucom.2020.05.126__Neurocomputing. Elsevier, 2021.https://doi.org/10.1016/j.neucom.2020.05.126 .

Tkadik, Gasper, and Thomas Gregor. “The Many Bits of Positional Information.”https://doi.org/10.1242/dev.176065__Development. The Company of Biologists, 2021.https://doi.org/10.1242/dev.176065 .

Mlynarski, Wiktor F, and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.”https://doi.org/10.1038/s41593-021-00846-0__Nature Neuroscience. Springer Nature, 2021.https://doi.org/10.1038/s41593-021-00846-0 .

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.”https://doi.org/10.1021/acsami.1c09850__ACS Applied Materials and Interfaces. American Chemical Society, 2021.https://doi.org/10.1021/acsami.1c09850 .

Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband Signals.”https://doi.org/10.1109/TSP.2021.3087899__IEEE Transactions on Signal Processing. Institute of Electrical and Electronics Engineers, 2021.https://doi.org/10.1109/TSP.2021.3087899 .

Chalk, Matthew J, Gasper Tkadik, and Olivier Marre. “Inferring the Function Performed by a Recurrent Neural Network.”https://doi.org/10.1371/journal.pone.0248940__PLoS ONE. Public Library of Science, 2021.https://doi.org/10.1371/journal.pone.0248940 .

Kavcic, Bor, Gasper Tkadik, and Mark Tobias Bollenbach. “Minimal Biophysical Model of Combined Antibiotic Action.”https://doi.org/10.1371/journal.pcbi.1008529__PLOS Computational Biology. Public Library of Science, 2021.https://doi.org/10.1371/journal.pcbi.1008529 .

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.”https://doi.org/10.7554/elife.65993__ELife. eLife Sciences Publications, 2021.https://doi.org/10.7554/elife.65993 .

Mlynarski, Wiktor F, Michal Hledik, Thomas R Sokolowski, and Gasper Tkadik. “Statistical Analysis and Optimality of Neural Systems.”https://doi.org/10.1016/j.neuron.2021.01.020__Neuron. Cell Press, 2021.https://doi.org/10.1016/j.neuron.2021.01.020 .

Nardin, Michele, Jozsef L Csicsvari, Gasper Tkadik, and Cristina Savin. “The Structure of Hippocampal C Interactions Optimizes Spatial Coding across Experience.”https://doi.org/10.1101/2021.09.28.460602__BioRxiv. Cold Spring Harbor Laboratory, n.d.https://doi.org/10.1101/2021.09.28.460602 .

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.”https://doi.org/10.1051/epjconf/202023000005__EPJ Web of Conferences. EDP Sciences, 2020.https://doi.org/10.1051/epjconf/202023000005 .

Narasimhan, Madhumitha, Alexander J Johnson, Roshan Prizak, Walter Kaufmann, Shutang Tan, Barbara E Casillas Perez, and Jií Friml. “Evolutionarily Unique Mechanistic Framework of Clathrin-Mediated Endocytosis in Plants.”https://doi.org/10.7554/eLife.52067__ELife. eLife Sciences Publications, 2020.https://doi.org/10.7554/eLife.52067 .

Grah, Rok, and Tamar Friedlander. “Distribution of Crosstalk Values.”https://doi.org/10.1371/journal.pcbi.1007642.s003__Public Library of Science, 2020.https://doi.org/10.1371/journal.pcbi.1007642.s003 .

Grah, Rok, and Tamar Friedlander. “Supporting Information.”https://doi.org/10.1371/journal.pcbi.1007642.s001__Public Library of Science, 2020.https://doi.org/10.1371/journal.pcbi.1007642.s001 .

Berry, Michael J., and Gasper Tkadik. “Clustering of Neural Activity: A Design Principle for Population Codes.”https://doi.org/10.3389/fncom.2020.00020__Frontiers in Computational Neuroscience. Frontiers, 2020.https://doi.org/10.3389/fncom.2020.00020 .

Maoz, Ori, Gasper Tkadik, Mohamad Saleh Esteki, Roozbeh Kiani, and Elad Schneidman. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.”https://doi.org/10.1073/pnas.1912804117__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 .

Rizzo, Rossella, Xiyun Zhang, Jilin W.J.L. Wang, Fabrizio Lombardi, and Plamen Ch Ivanov. “Network Physiology of Cortico–Muscular Interactions.”https://doi.org/10.3389/fphys.2020.558070__Frontiers in Physiology. Frontiers, 2020.https://doi.org/10.3389/fphys.2020.558070 .

Grah, Rok, Benjamin Zoller, and Gasper Tkadik. “Nonequilibrium Models of Optimal Enhancer Function.”https://doi.org/10.1073/pnas.2006731117__PNAS. National Academy of Sciences, 2020.https://doi.org/10.1073/pnas.2006731117 .

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.”https://doi.org/10.1523/jneurosci.1278-19.2019__Journal of Neuroscience. Society for Neuroscience, 2020.https://doi.org/10.1523/jneurosci.1278-19.2019 .

Grah, Rok. “Gene Regulation across Scales – How Biophysical Constraints Shape Evolution.”https://doi.org/10.15479/AT:ISTA:8155__Institute of Science and Technology Austria, 2020.https://doi.org/10.15479/AT:ISTA:8155 .

Grah, Rok, Benjamin Zoller, and Gasper Tkadik. “Normative Models of Enhancer Function.”https://doi.org/10.1101/2020.04.08.029405__BioRxiv. Cold Spring Harbor Laboratory, 2020.https://doi.org/10.1101/2020.04.08.029405 .

Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.”https://doi.org/10.1371/journal.pcbi.1007642__PLOS Computational Biology. Public Library of Science, 2020.https://doi.org/10.1371/journal.pcbi.1007642 .

Grah, Rok, and Tamar Friedlander. “Maximizing Crosstalk.”https://doi.org/10.1371/journal.pcbi.1007642.s002__Public Library of Science, 2020.https://doi.org/10.1371/journal.pcbi.1007642.s002 .

Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.’”https://doi.org/10.15479/AT:ISTA:8097__Institute of Science and Technology Austria, 2020.https://doi.org/10.15479/AT:ISTA:8097 .

Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Minimal Biophysical Model of Combined Antibiotic Action.’”https://doi.org/10.15479/AT:ISTA:8930__Institute of Science and Technology Austria, 2020.https://doi.org/10.15479/AT:ISTA:8930 .

Grah, Rok. “Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation.”https://doi.org/10.15479/AT:ISTA:7383__Institute of Science and Technology Austria, 2020.https://doi.org/10.15479/AT:ISTA:7383 .

Kavcic, Bor. “Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology.”https://doi.org/10.15479/AT:ISTA:8657__Institute of Science and Technology Austria, 2020.https://doi.org/10.15479/AT:ISTA:8657 .

Kavcic, Bor, Gasper Tkadik, and Mark Tobias Bollenbach. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.”https://doi.org/10.1038/s41467-020-17734-z__Nature Communications. Springer Nature, 2020.https://doi.org/10.1038/s41467-020-17734-z .

Kavcic, Bor, Gasper Tkadik, and Mark Tobias Bollenbach. “A Minimal Biophysical Model of Combined Antibiotic Action.”https://doi.org/10.1101/2020.04.18.047886__BioRxiv. Cold Spring Harbor Laboratory, 2020.https://doi.org/10.1101/2020.04.18.047886 .

Tomanek, Isabella, Rok Grah, M. Lagator, A. M. C. Andersson, Jonathan P Bollback, Gasper Tkadik, and Calin C Guet. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.”https://doi.org/10.1038/s41559-020-1132-7__Nature Ecology &; Evolution. Springer Nature, 2020.https://doi.org/10.1038/s41559-020-1132-7 .

Bialek, William, Thomas Gregor, and Gasper Tkadik. “Action at a Distance in Transcriptional Regulation.” ArXiv:1912.08579. ArXiv, n.d.