@phdthesis{20357,
  author       = {Ruzickova, Natalia},
  isbn         = {978-3-99078-066-4},
  issn         = {2663-337X},
  keywords     = {gene regulation, networks, omnigenic model, pancreas, collective behaviour},
  pages        = {160},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Effect propagation in biological networks}},
  doi          = {10.15479/AT-ISTA-20357},
  year         = {2025},
}

@article{20664,
  abstract     = {Conference travel contributes to the climate footprint of academic research. Here, we provide a quantitative estimate of the carbon emissions associated with conference attendance by analyzing travel data from participants of 10 international conferences in the field of magnetic resonance, namely EUROMAR, ENC and ICMRBS. We find that attending a EUROMAR conference produces, on average, more than 1 t CO2 eq.. For the analyzed conferences outside Europe, the corresponding value is about 2–3 times higher, on average, with intercontinental trips amounting to up to 5 t. We compare these conference-related emissions to other activities associated with research and show that conference travel is a substantial portion of the total climate footprint of a researcher in magnetic resonance. We explore several strategies to reduce these emissions, including the impact of selecting conference venues more strategically and the possibility of decentralized conferences. Through a detailed comparison of train versus air travel – accounting for both direct and infrastructure-related emissions – we demonstrate that train travel offers considerable carbon savings. These data may provide a basis for strategic choices of future conferences in the field and for individuals deciding on their conference attendance.},
  author       = {Kapoor, Lucky and Ruzickova, Natalia and Zivadinovic, Predrag and Leitner, Valentin and Sisak, Maria A and Mweka, Cecelia N and Dobbelaere, Jeroen A and Katsaros, Georgios and Schanda, Paul},
  issn         = {2699-0016},
  journal      = {Magnetic Resonance},
  number       = {2},
  pages        = {243--256},
  publisher    = {Copernicus Publications},
  title        = {{Quantifying the carbon footprint of conference travel: The case of NMR meetings}},
  doi          = {10.5194/mr-6-243-2025},
  volume       = {6},
  year         = {2025},
}

@article{18525,
  abstract     = {As their statistical power grows, genome-wide association studies (GWAS) have identified an increasing number of loci underlying quantitative traits of interest. These loci are scattered throughout the genome and are individually responsible only for small fractions of the total heritable trait variance. The recently proposed omnigenic model provides a conceptual framework to explain these observations by postulating that numerous distant loci contribute to each complex trait via effect propagation through intracellular regulatory networks. We formalize this conceptual framework by proposing the “quantitative omnigenic model” (QOM), a statistical model that combines prior knowledge of the regulatory network topology with genomic data. By applying our model to gene expression traits in yeast, we demonstrate that QOM achieves similar gene expression prediction performance to traditional GWAS with hundreds of times less parameters, while simultaneously extracting candidate causal and quantitative chains of effect propagation through the regulatory network for every individual gene. We estimate the fraction of heritable trait variance in cis- and in trans-, break the latter down by effect propagation order, assess the trans- variance not attributable to transcriptional regulation, and show that QOM correctly accounts for the low-dimensional structure of gene expression covariance. We furthermore demonstrate the relevance of QOM for systems biology, by employing it as a statistical test for the quality of regulatory network reconstructions, and linking it to the propagation of nontranscriptional (including environmental) effects.},
  author       = {Ruzickova, Natalia and Hledik, Michal and Tkačik, Gašper},
  issn         = {1091-6490},
  journal      = {Proceedings of the National Academy of Sciences of the United States of America},
  number       = {44},
  publisher    = {National Academy of Sciences},
  title        = {{Quantitative omnigenic model discovers interpretable genome-wide associations}},
  doi          = {10.1073/pnas.2402340121},
  volume       = {121},
  year         = {2024},
}

@article{9255,
  abstract     = {Our ability to trust that a random number is truly random is essential for fields as diverse as cryptography and fundamental tests of quantum mechanics. Existing solutions both come with drawbacks—device-independent quantum random number generators (QRNGs) are highly impractical and standard semi-device-independent QRNGs are limited to a specific physical implementation and level of trust. Here we propose a framework for semi-device-independent randomness certification, using a source of trusted vacuum in the form of a signal shutter. It employs a flexible set of assumptions and levels of trust, allowing it to be applied in a wide range of physical scenarios involving both quantum and classical entropy sources. We experimentally demonstrate our protocol with a photonic setup and generate secure random bits under three different assumptions with varying degrees of security and resulting data rates.},
  author       = {Pivoluska, Matej and Plesch, Martin and Farkas, Máté and Ruzickova, Natalia and Flegel, Clara and Valencia, Natalia Herrera and Mccutcheon, Will and Malik, Mehul and Aguilar, Edgar A.},
  issn         = {2056-6387},
  journal      = {npj Quantum Information},
  publisher    = {Springer Nature},
  title        = {{Semi-device-independent random number generation with flexible assumptions}},
  doi          = {10.1038/s41534-021-00387-1},
  volume       = {7},
  year         = {2021},
}

@article{8602,
  abstract     = {Collective cell migration offers a rich field of study for non-equilibrium physics and cellular biology, revealing phenomena such as glassy dynamics, pattern formation and active turbulence. However, how mechanical and chemical signalling are integrated at the cellular level to give rise to such collective behaviours remains unclear. We address this by focusing on the highly conserved phenomenon of spatiotemporal waves of density and extracellular signal-regulated kinase (ERK) activation, which appear both in vitro and in vivo during collective cell migration and wound healing. First, we propose a biophysical theory, backed by mechanical and optogenetic perturbation experiments, showing that patterns can be quantitatively explained by a mechanochemical coupling between active cellular tensions and the mechanosensitive ERK pathway. Next, we demonstrate how this biophysical mechanism can robustly induce long-ranged order and migration in a desired orientation, and we determine the theoretically optimal wavelength and period for inducing maximal migration towards free edges, which fits well with experimentally observed dynamics. We thereby provide a bridge between the biophysical origin of spatiotemporal instabilities and the design principles of robust and efficient long-ranged migration.},
  author       = {Boocock, Daniel R and Hino, Naoya and Ruzickova, Natalia and Hirashima, Tsuyoshi and Hannezo, Edouard B},
  issn         = {1745-2481},
  journal      = {Nature Physics},
  pages        = {267--274},
  publisher    = {Springer Nature},
  title        = {{Theory of mechanochemical patterning and optimal migration in cell monolayers}},
  doi          = {10.1038/s41567-020-01037-7},
  volume       = {17},
  year         = {2021},
}

@article{7622,
  abstract     = {The International Young Physicists' Tournament (IYPT) continued in 2018 in Beijing, China and 2019 in Warsaw, Poland with its 31st and 32nd editions. The IYPT is a modern scientific competition for teams of high school students, also known as the Physics World Cup. It involves long-term theoretical and experimental work focused on solving 17 publicly announced open-ended problems in teams of five. On top of that, teams have to present their solutions in front of other teams and a scientific jury, and get opposed and reviewed by their peers. Here we present a brief information about the competition with a specific focus on one of the IYPT 2018 tasks, the 'Ring Oiler'. This seemingly simple mechanical problem appeared to be of such a complexity that even the dozens of participating teams and jurying scientists were not able to solve all of its subtleties.},
  author       = {Plesch, Martin and Plesník, Samuel and Ruzickova, Natalia},
  issn         = {1361-6404},
  journal      = {European Journal of Physics},
  number       = {3},
  publisher    = {IOP Publishing},
  title        = {{The IYPT and the 'Ring Oiler' problem}},
  doi          = {10.1088/1361-6404/ab6414},
  volume       = {41},
  year         = {2020},
}