@article{21232,
  abstract     = {<jats:title>Abstract</jats:title>
                  <jats:p>In this paper, we consider a simple class of stratified spaces – 2-complexes. We present an algorithm that learns the abstract structure of an embedded 2-complex from a point cloud sampled from it. We use tools and inspiration from computational geometry, algebraic topology, and topological data analysis and prove the correctness of the identified abstract structure under assumptions on the embedding.</jats:p>},
  author       = {Bleile, Yossi},
  issn         = {2730-9657},
  journal      = {La Matematica},
  publisher    = {Springer Nature},
  title        = {{Towards stratified space learning: 2-complexes}},
  doi          = {10.1007/s44007-025-00183-9},
  volume       = {5},
  year         = {2026},
}

@phdthesis{21957,
  abstract     = {This thesis investigates algorithmic certification and approximation methods for degenerate semidefinite programs (SDPs) and the singular roots of polynomial systems. In the first part, we present a hybrid symbolic-numeric algorithm for certifying the feasibility of weakly feasible, degenerate SDPs. By reformulating linear matrix inequalities (LMIs) into a structured polynomial system via facial reduction and incidence varieties, we guarantee the existence of an isolated exact solution. This algebraic reduction enables the certification of maximum-rank numerical approximations using methods from algebraic geometry.

In the second part, we address the severe ill-conditioning and loss of quadratic convergence that plague standard path-tracking methods near isolated singular roots. To overcome this, we propose tracking algorithms that achieve superlinear convergence without the computational bloat characteristic of classical deflation techniques. By modeling the solution path as a generalized fractional Puiseux series, our approach combines an explicitly derived algebraic predictor with a localized hyperplane desingularization phase during the corrector step. Furthermore, we introduce a continuous path-limit method and an extension of the geometric sequence rule to directly extract exact fractional exponents. This bypasses traditional heuristic trial-and-error methods and explicitly accommodates sparse series expansions. Numerical experiments confirm that our method significantly reduces the cumulative number of matrix inversions while achieving high-accuracy root approximations, even for heavily degenerate systems exhibiting higher coranks.},
  author       = {Zapata, Jeferson},
  isbn         = {978-3-99078-079-4},
  issn         = {2663-337X},
  pages        = {89},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Overcoming degeneracy and singularity : Techniques for semidefinite programs and homotopy continuation endgames}},
  doi          = {10.15479/AT-ISTA-21957},
  year         = {2026},
}

@phdthesis{21918,
  author       = {Khudiakova, Kseniia},
  issn         = {2663-337X},
  pages        = {89},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{How epistasis and purifying selection shape genetic diversity}},
  doi          = {10.15479/AT-ISTA-21918},
  year         = {2026},
}

@unpublished{21968,
  abstract     = {Balancing selection, a form of selection that maintains genetic diversity, is difficult to detect, and the importance of balancing selection for the maintenance of genetic variation may be larger than often assumed. We model the possibility that the diversity-promoting effects of balancing selection extend to other loci that show sign epistasis with a locus under balancing selection. Rather than focusing on overdominance, as was done in previous efforts, we explore the effects of negative frequency dependence and show that this has important effects on the conditions under which the diversity-promoting effect of epistasis can occur in diploids. Our results show that not only recombination rate but also the dominance of sign epistasis are key parameters that determine the maintenance of polymorphism beyond the locus under direct balancing selection. We suggest that the effect we explore may play a significant role, especially when balancing selection acts on major effect loci.},
  author       = {Khudiakova, Kseniia and Barton, Nicholas H and Arnqvist, Goran},
  booktitle    = {bioRxiv},
  title        = {{Sign epistasis extends the effects of balancing selection on genetic diversity}},
  doi          = {10.1101/2025.04.09.647826},
  year         = {2026},
}

@unpublished{21962,
  abstract     = {The generation of faithful cell-type diversity and correct projection neuron numbers is essential for cerebral cortex development. Corticogenesis is however susceptible to genetic interference of critical signaling pathways, including mutations in Mtor/Rptor that lead to microcephaly. How the loss of Rptor/mTORC1 function affects cortical developmental programs, at single cell level, is still unknown. Here, we utilized Mosaic Analysis with Double Markers (MADM) technology to probe Rptor gene function upon sparse single cell- or global tissue-wide ablation. We found that tissue-wide effects drive the etiology of cortical microcephaly upon loss of Rptor, rather than deficits in projection neuron genesis. Conversely, Rptor function is cell-autonomously required for postnatal projection neuron survival in a highly cell-type-specific manner. Collectively, our results suggest that the fine balance of precise cell-type-specific cell-autonomous Rptor/mTORC1 function in concert with non-cell-autonomous tissue-wide effects is essential for the development of a properly-sized cerebral cortex with accurate projection neuron diversity.},
  author       = {Villalba Requena, Ana and Beattie, Robert J and Pauler, Florian and Streicher, Carmen and Miranda, Osvaldo and Krausgruber, Thomas and Senekowitsch, Martin and Farlik, Matthias and Bock, Christoph and Rülicke, Thomas and Hippenmeyer, Simon},
  booktitle    = {bioRxiv},
  title        = {{Mtor/Rptor function globally prevents cortical microcephaly and cell-autonomously promotes postnatal neuron survival in cell type specific manner}},
  doi          = {10.64898/2026.05.01.722172},
  year         = {2026},
}

@article{21955,
  abstract     = {AgRP neurons cause hunger, the drive to seek and consume food. Their activation by fasting is key for survival and is thought to be triggered by feedback when energy stores are low. However, we know that environmental cues can also regulate AgRP neurons since cues that predict future food intake rapidly inhibit AgRP neurons, but is the converse true: can the prediction of future fasting rapidly activate AgRP neurons? Here, we show in mice that such rapid fasting activation of AgRP neurons does occur. This rapid activation is driven by excitatory input from paraventricular hypothalamic (PVH) neurons expressing Sim2, which are bidirectionally sensitive to predictions of future energy state. Thus, cognitively processed contextual information conveyed by PVHSim2 neurons strongly activates AgRP neurons. Lastly, chronic silencing of PVHSim2 neurons causes persistent hypophagia. This PVHSim2-to-AgRP-neuron circuit, by anticipating and preventing negative energy balance, provides an important new dimension of hunger regulation.},
  author       = {Walker, Samuel J. and Lowenstein, Elijah D. and Douglass, Amelia May Barnett and Thomas, Callum M.P. and Madara, Joseph C. and Kucukdereli, Hakan and Barbosa-Meillon, Eunice A. and Tao, Jenkang and Resch, Jon M. and Lowell, Bradford B.},
  issn         = { 1097-4199},
  journal      = {Neuron},
  keywords     = {hunger, hypothalamus, AGRP neurons, neuroscience, metabolism, homeostasis, feeding, food intake, energy balance, appetite},
  publisher    = {Elsevier},
  title        = {{A hypothalamic circuit for anticipating future changes in energy balance}},
  doi          = {10.1016/j.neuron.2026.05.010},
  year         = {2026},
}

@misc{21960,
  abstract     = {Solitons - localized wave packets that travel without spreading - play a central role in understanding transport and properties of nonlinear systems. In quantum many-body systems, however, such robust excitations are typically destroyed by thermalization. Here, we theoretically demonstrate the existence of solitonic excitations in high-energy states of Rydberg atom chains in the regime of strong nearest-neighbor Rydberg blockade. 
These localized wave packets propagate directionally atop a special class of reviving initial states related to quantum many-body scars and are capable of carrying energy. Exhibiting long coherence times, these states constitute a form of non-ergodic quantum dynamics and can be efficiently implemented on Rydberg atom simulators. In this work, in addition to a phenomenological description of solitons, we identify their counterpart in a classical nonlinear dynamical system, demonstrate their potential use in quantum information transfer, and conjecture their relevance for anomalous energy transport reported in numerical studies of Rydberg atom arrays.},
  author       = {Kerschbaumer, Aron},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Research Data: "Quasi-solitons in Rydberg atom chains"}},
  doi          = {10.15479/AT-ISTA-21960},
  year         = {2026},
}

@misc{21971,
  abstract     = {A Rust library for analyzing dendritic structures using quadric matrices. This project provides efficient tools for representing dendritic trees, computing quadric error metrics, and visualizing eigenvalue distributions on hexagonal plots.

This library implements quadric-based geometric analysis of dendritic structures, commonly found in neuroscience applications. Key features include:

Tree data structures: Hierarchical vertex and edge representations for dendritic trees
Quadric matrices: Computation of quadric error metrics for edges and vertices
Visualisation: Hexagonal plot generation using NormPolar transformations
Interactive tools: Desktop application with plotting capabilities},
  author       = {Bleile, Yossi and Cortinovis, Emanuele},
  keywords     = {quadratics, mathematics, dendrites, geometry, topology},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Quadrix}},
  doi          = {10.15479/AT-ISTA-21971},
  year         = {2026},
}

@article{21342,
  abstract     = {JWST has revealed a stunning population of bright galaxies at surprisingly early epochs, z > 10,
where few such sources were expected. Here we present the most distant example of this class yet – MoM-z14, a luminous (MUV = −20.2) source in the COSMOS legacy field at zspec = 14.44+0.02−0.02 that expands the observational frontier to a mere 280 million years after the Big Bang. The redshift is confirmed with NIRSpec/prism spectroscopy through a sharp Lyman-α break and ≈ 3σ detections of five rest-UV emission lines. The number density of bright zspec ≈ 14 − 15 sources implied by our “Mirage or Miracle” survey spanning ≈ 350 arcmin2 is > 100× larger (182+329 −105×) than pre-JWST consensus models. The high EWs of UV lines (≈15−35˚A) signal a rising star-formation history, with a ≈10× increase in the last 5 Myr (SFR5Myr/SFR50Myr = 9.9 +3.0 −5.8). The source is extremely compact (circularized re = 74+15
−12 pc), and yet elongated (b/a = 0.25+0.11−0.06), suggesting an AGN is not the dominant source of UV light. The steep UV slope (β = −2.5 +0.2 −0.2) implies negligible dust attenuation
and a young stellar population. The absence of a strong damping wing provides tentative evidence that the immediate surroundings of MoM-z14 may be partially ionized at a redshift where virtually every reionization model predicts a ≈ 100% neutral fraction. The nitrogen emission and highly supersolar [N/C]> 1 hint at an abundance pattern similar to local globular clusters that may have once hosted luminous supermassive stars. Since this abundance pattern is also common among the most ancient stars born in the Milky Way, we may be directly witnessing the formation of such stars in dense clusters, connecting galaxy evolution across the entire sweep of cosmic time. },
  author       = {Naidu, Rohan P. and Oesch, Pascal A. and Brammer, Gabriel and Weibel, Andrea and Li, Yijia and Matthee, Jorryt J and Chisholm, John and Pollock, Clara L. and Heintz, Kasper E. and Johnson, Benjamin D. and Shen, Xuejian and Hviding, Raphael E. and Leja, Joel and Tacchella, Sandro and Ganguly, Arpita and Witten, Callum and Atek, Hakim and Belli, Sirio and Bose, Sownak and Bouwens, Rychard and Dayal, Pratika and Decarli, Roberto and De Graaff, Anna and Fudamoto, Yoshinobu and Giovinazzo, Emma and Greene, Jenny E. and Illingworth, Garth and Inoue, Akio K. and Kane, Sarah G. and Labbe, Ivo and Leonova, Ecaterina and Marques-Chaves, Rui and Meyer, Romain A. and Nelson, Erica J. and Roberts-Borsani, Guido and Schaerer, Daniel and Simcoe, Robert A. and Stefanon, Mauro and Sugahara, Yuma and Toft, Sune and Van Der Wel, Arjen and Van Dokkum, Pieter and Walter, Fabian and Watson, Darach and Weaver, John R. and Whitaker, Katherine E.},
  issn         = {2565-6120},
  journal      = {The Open Journal of Astrophysics},
  publisher    = {Maynooth Academic Publishing},
  title        = {{A cosmic miracle: A remarkably luminous galaxy at zspec = 14.44 confirmed with JWST}},
  doi          = {10.33232/001c.156033},
  volume       = {9},
  year         = {2026},
}

@article{21657,
  abstract     = {We compare three global kilometer-scale models (ICON, IFS and NICAM) to clarify the advantages and challenges of high-resolution global weather and climate modeling, using different approaches to represent convection, from fully parameterized to fully explicit. Our analysis focuses on tropical precipitation characteristics spanning a wide range of spatio-temporal scales—including the diurnal cycle, extreme precipitation, convective organization, and the Madden-Julian Oscillation (MJO)—along with interactions between convection and the thermodynamic environment. All three models commonly show weaker convective organization with smaller precipitation cells than observed, though the strength of the bias varies by model. This diversity is introduced by differences in the representation of (a) convective initiation affected by the convective sensitivity to moisture and (b) tropospheric moistening associated with deep convection. Models with stronger thermodynamic-convection coupling increase environmental moisture near convection, thereby enhancing convective organization. This has important upscale effects on the MJO; while IFS and NICAM capture its eastward propagation well, ICON has difficulty reproducing it. The amplitudes and phases of precipitation diurnal cycles over land show much greater disagreement among the models than over ocean, influenced by how convection is initiated. Biases in rain evaporation and cold pool formation hinder the propagation of mesoscale convection, leading to errors such as the misrepresentation of nocturnal convection moving off the coast of Sumatra in IFS and ICON. These results highlight the importance of thermodynamic-convection coupling in realistically simulating tropical convection across scales. To improve this coupling, kilometer-scale models require better representation of the interaction between resolved convection and three-dimensional turbulent mixing.},
  author       = {Takasuka, Daisuke and Becker, Tobias and Bao, Jiawei},
  issn         = {1942-2466},
  journal      = {Journal of Advances in Modeling Earth Systems},
  number       = {3},
  publisher    = {Wiley},
  title        = {{Precipitation characteristics and thermodynamic-convection coupling in global kilometer-scale simulations}},
  doi          = {10.1029/2025MS005343},
  volume       = {18},
  year         = {2026},
}

@article{21980,
  abstract     = {Despite significant progress in the field of molecular electronics over the last two decades, the quantitative prediction of metal-molecule-metal junction conductance remains a challenge. The standard computational framework combines density functional theory (DFT) with nonequilibrium Green’s functions (NEGF) using low-rung exchange-correlation functionals such as PBE, which overestimate the conductances. More advanced correction methods exist but require complex workflows and high computational cost, limiting their accessibility. Here, we introduce a physically motivated approach that approximates results obtained with high-rung functionals. Our method fits the PBE-calculated transmission to a Breit-Wigner form and subsequently refines the fit parameters using molecular orbital energies and metal densities of states computed for the isolated subsystems with high-rung functionals. This approach is applicable to a broad range of molecular junctions yielding conductance values in quantitative agreement with experiments. Our approach is simple, low-cost, and accurate, making it well-suited for routine and large-scale prediction of single-molecule junction conductance.},
  author       = {Gulyaev, Artem and Hazarika, Jyotisman and Liu, Zhen-Fei and Venkataraman, Latha},
  issn         = {1530-6992},
  journal      = {Nano Letters},
  number       = {22},
  pages        = {7429–7434},
  publisher    = {American Chemical Society},
  title        = {{A computationally efficient and accurate method for predicting conductance of single-molecule junctions}},
  doi          = {10.1021/acs.nanolett.6c01462},
  volume       = {26},
  year         = {2026},
}

@article{21983,
  abstract     = {Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yielded TF-DNA interaction models that predict how strongly an individual TF binds arbitrary DNA sequences and how individual binding events on the CRE combine to affect gene expression. These insights can be synthesized into a global, biophysically realistic, and quantitative genotype–phenotype map for gene regulation, a ‘holy grail’ for the application of evolutionary theory. A global map provides a rare opportunity to simulate the long-term evolution of regulatory sequences and pose several fundamental questions: How long does it take to evolve CREs de novo? How many non-trivial regulatory functions exist in sequence space? How connected are they? For which regulatory architecture is CRE evolution most rapid and evolvable? In this article, the first of a two-part series, we briefly review the pertinent modeling and simulation efforts for a unique system that enables close, quantitative, and mechanistic links between biophysics, as well as systems, synthetic, and evolutionary biology.},
  author       = {Mascolo, Elia and Körei, Reka E and Herrera-Álvarez, Santiago and Guet, Calin C and Crocker, Justin and Tkačik, Gašper},
  issn         = {1879-0380},
  journal      = {Current Opinion in Genetics & Development},
  publisher    = {Elsevier},
  title        = {{Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps}},
  doi          = {10.1016/j.gde.2026.102483},
  volume       = {99},
  year         = {2026},
}

@article{21982,
  abstract     = {A floating Leidenfrost droplet exhibits curvature inversion of its underside, due to the balance of vapor pressure and surface tension. Using interferometric imaging, we find different behavior for a levitated hydrogel sphere. Curvature inversion is observed briefly just after deposition, but quickly gives way to a steady state with no inversion. We show the essential role of vaporization in shaping the underbelly of the hydrogel, where changes due to direct mass loss are more significant than the balance of vapor pressure and elastic forces.},
  author       = {Diaz Melian, Vicente L and Lenton, Isaac C and Binysh, Jack and Souslov, Anton and Waitukaitis, Scott R},
  issn         = {2470-0053},
  journal      = {Physical Review E},
  number       = {5},
  publisher    = {American Physical Society},
  title        = {{Geometry of the vapor layer under a Leidenfrost hydrogel sphere}},
  doi          = {10.1103/m7gr-2t6j},
  volume       = {113},
  year         = {2026},
}

@article{21985,
  abstract     = {Upon infecting a bacterial cell, temperate phages make a decision between lysis and lysogeny. While research has previously explored how phages sense environmental information to make this choice, most studies have focused on modelling known mechanisms that impact the decision. These mechanisms tell us what environmental information the phage does respond to, but not what it should respond to, as the signals sensed by the phage may serve as proxies for other sources of information. Here, using a mechanism-agnostic population dynamics model, we find that irreversible phage binding to lysogens protects sensitive host cells from infection. This results in lysogens being an additional environmental factor that the phage should sense while making its decision to undergo lysis or lysogeny. Using this model, we derive a responsive lysogeny probability for phages that respond to both cell and lysogen densities optimized towards invading phage-occupied systems, and show that it is more capable of invading and resisting invasion than phage with fixed lysogeny probabilities across different environmental conditions.},
  author       = {Wu, Bryan and Guet, Calin C},
  issn         = {1558-5646},
  journal      = {Evolution},
  number       = {6},
  pages        = {1365--1373},
  publisher    = {Oxford University Press},
  title        = {{Responsive lysogeny under nonproductive phage binding}},
  doi          = {10.1093/evolut/qpag061},
  volume       = {80},
  year         = {2026},
}

@unpublished{21963,
  abstract     = {The cerebral cortex consists of immense numbers of neuronal and glial cell-types derived from radial glial progenitor (RGP) cells. How RGPs generate appropriate quantities of distinct cortical cell-types to safeguard a brain of correct size, is not well understood. However, genetic aberration in human, including mutations in PTEN, lead to cortical malformation such as macrocephaly, albeit with unknown etiology. Here we utilized Mosaic Analysis with Double Markers (MADM)-based clonal analysis and single cell phenotyping to decipher the role of Pten in neurogenic and gliogenic RGP lineage progression during cortical ontogeny. While neurogenic RGP lineage progression and projection neuron production was moderately altered in the absence of Pten, cortical astrocyte production was drastically increased. Through genetic epistasis experiments we show that the loss of Pten uncouples astrocyte generation from essential growth factor signaling hubs, funneling into MAPK. Collectively, our results suggest that Pten regulates RGP lineage progression with distinct sequential functions in cortical projection neurogenesis and astrocyte production to ensure the emergence of a correctly-sized cerebral cortex.},
  author       = {Miranda, Osvaldo and Contreras, Ximena and Pauler, Florian and Davaatseren, Amarbayasgalan and Amberg, Nicole and Streicher, Carmen and Villalba Requena, Ana and Heger, Anna-Magdalena and Marie, Corentine and Hassan, Bassem A. and Rülicke, Thomas and Hippenmeyer, Simon},
  booktitle    = {bioRxiv},
  title        = {{Pten orchestrates neurogenic radial glia lineage progression and tunes neocortical astrocyte production}},
  doi          = {10.64898/2026.05.01.722191},
  year         = {2026},
}

@article{21981,
  abstract     = {For Hamiltonian actions of semidirect products G = FxH, we study 2-cocycles arising from residual Hamiltonian actions of F on Hamiltonian reductions for H. The motivation comes from the study of Teichmüller spaces for surfaces with boundary, which carry Hamiltonian actions of the Virasoro algebra. In this paper, we give a general setup for the problem, and we suggest an easier way to obtain the Gelfand-Fuchs 2-cocycles for Hamiltonian actions on Teichmüller spaces.},
  author       = {Goncharov, Viacheslav},
  issn         = {1879-1662},
  journal      = {Journal of Geometry and Physics},
  publisher    = {Elsevier},
  title        = {{An easier way to compute 2-cocycles coming from a reduction for semidirect products}},
  doi          = {10.1016/j.geomphys.2026.105878},
  volume       = {227},
  year         = {2026},
}

@article{21472,
  abstract     = {We study the ground state energy of a gas of spin 1/2 fermions with repulsive short-range interactions. We derive an upper bound that agrees, at low density e, with the Huang–Yang conjecture. The latter captures the first three terms in an asymptotic low-density expansion, and in particular the Huang–Yang correction term of order e^7/3. Our trial state is constructed using an adaptation of the bosonic Bogoliubov theory to the Fermi system, where the correlation structure of fermionic particles is incorporated by quasi-bosonic Bogoliubov transformations. In the latter, it is important to consider a modified zero-energy scattering equation that takes into account the presence of the Fermi sea, in the spirit of the Bethe–Goldstone equation.},
  author       = {Giacomelli, Emanuela L. and Hainzl, Christian and Nam, Phan Thành and Seiringer, Robert},
  issn         = {1097-0312},
  journal      = {Communications on Pure and Applied Mathematics},
  publisher    = {Wiley},
  title        = {{The Huang–Yang formula for the low-density Fermi gas: Upper bound}},
  doi          = {10.1002/cpa.70040},
  year         = {2026},
}

@article{21767,
  abstract     = {The involvement of non-scientific staff in discussions about animal welfare and scientific quality is essential for biomedical research progress. In this study, we developed a survey to collect the self-perception of animal care staff (ACS) and laboratory technicians about their involvement in scientific planning and conduct. Participants were contacted to complete an anonymous online questionnaire. We obtained 850 responses, mainly from Europe: 564 from ACS and 286 from laboratory technicians. Job satisfaction was assessed as positive by ACS and laboratory technicians despite the low frequency of culture of care activities and mental health meetings. Both groups expressed their desire to be trained in research planning and conduct; however, regular training was not reported. In addition, the inability to act on animal welfare concerns owing to experimental reasons was reported by both groups. Over half of the participants felt valued and appreciated by the lead scientists or animal facility manager; however, it is not clear how they are acknowledged, as their names on the authors list or in the manuscript acknowledgments are barely included. Our results indicated that involvement of ACS and laboratory technicians in planning and conducting studies would improve their understanding of how experiments are done, and therefore communication processes, work satisfaction, animal welfare, and scientific quality. Finally, we provided recommendations to improve the engagement of ACS and laboratory technicians in discussions about animal research planning and conduct.},
  author       = {Gonzalez-Uarquin, Fernando and Jirkof, Paulin and Bert, Bettina and Hawkins, Penny and Angelovski, Ljupco and Baumgart, Jan and Baumgart, Nadine and Cevik, Özge S. and Franco, Nuno H. and Horata, Erdal and Kaura, Rohish and Neuhaus, Winfried and Riso, Brigida and Smith, Adrian J. and Sotiropoulos, Athanassia and Vitale, Augusto and Schober, Sophie},
  issn         = {1758-1117},
  journal      = {Laboratory Animals},
  publisher    = {SAGE Publications},
  title        = {{Building bridges: Involvement of animal care staff and laboratory technicians in experimental planning and conduct of animal studies for better job satisfaction and science}},
  doi          = {10.1177/00236772251400976},
  year         = {2026},
}

@article{21759,
  abstract     = {Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yielded TF-DNA interaction models that predict how strongly an individual TF binds arbitrary DNA sequences and how individual binding events on the CRE combine to affect gene expression. These insights can be synthesized into a global, biophysically realistic, and quantitative genotype-phenotype (GP) map for gene regulation, a ‘holy grail’ for the application of evolutionary theory. A global map provides a rare opportunity to simulate the long-term evolution of regulatory sequences and pose several fundamental questions: How long does it take to evolve CREs de novo? How many non-trivial regulatory functions exist in sequence space? How connected are they? For which regulatory architecture is CRE evolution most rapid and evolvable? In this article, the second of a two-part series, we review the application of evolutionary concepts — epistasis, robustness, evolvability, tunability, plasticity, and bet-hedging — to the evolution of gene regulatory sequences. We then evaluate the potential for a unifying theory for the evolution of regulatory sequences and identify key open challenges.},
  author       = {Mascolo, Elia and Körei, Reka E and Borst, Noa O. and Barton, Nicholas H and Crocker, Justin and Tkačik, Gašper},
  issn         = {1879-0380},
  journal      = {Current Opinion in Genetics and Development},
  publisher    = {Elsevier},
  title        = {{Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges}},
  doi          = {10.1016/j.gde.2026.102472},
  volume       = {98},
  year         = {2026},
}

@article{21483,
  abstract     = {Embryogenesis in the model plant Arabidopsis thaliana provides a framework for understanding how cell polarity and patterning coordinate with hormonal signalling to establish the plant body plan. Following fertilisation, the zygote divides asymmetrically to generate apical and basal lineages, establishing the apical–basal axis that defines future shoot and root poles. Genetic and molecular analyses of classical mutants including gnom, monopteros (mp), bodenlos (bdl) and topless revealed that localised auxin biosynthesis, directional transport and downstream transcriptional responses are central to apical–basal axis establishment and organ initiation. The main components of this regulation are polarly localised PIN auxin transporters and downstream modules involving MONOPTEROS and WUSCHEL-RELATED HOMEOBOX transcription factors. Advances in microscopy have transformed the study of Arabidopsis embryogenesis: fluorescence-compatible clearing reagents and three-dimensional reconstructions now permit quantitative analyses of cell geometry, division orientation, and cytoskeletal dynamics. Live ovule imaging setups with confocal laser scanning and multiphoton microscopes enable real-time observation of embryo development, while laser-assisted cell ablation can be used to probe cell-to-cell communication and fate plasticity. Together, these methodological breakthroughs position Arabidopsis embryos as a prime model for dissecting the chemical and biophysical cues that shape plant development.},
  author       = {Babic, David and Zupunski, Milan and Friml, Jiří},
  issn         = {1469-8137},
  journal      = {New Phytologist},
  publisher    = {Wiley},
  title        = {{Imaging and genetic toolbox to study Arabidopsis embryogenesis}},
  doi          = {10.1111/nph.71072},
  year         = {2026},
}